library(readr)
library(dplyr)
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filter, lag
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and introduction to the package please type: help(metafor).library(devtools)Loading required package: usethislibrary(purrr)
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library(kableExtra)
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library(here)here() starts at /Users/sz/susi/garvan/Github/IMPC sexDiffs/mice_sex_diff_sydFunctions for preparing the data for meta analyses
calculate_population_stats <- function(mydata, min_individuals = 5) {
mydata %>%
group_by(population, strain_name, production_center, sex) %>%
summarise(
trait = parameter_name[1],
x_bar = mean(data_point),
x_sd = sd(data_point),
n_ind = n()
) %>%
ungroup() %>%
filter(n_ind > min_individuals) %>%
# Check both sexes present & filter those missing
group_by(population) %>%
mutate(
n_sex = n_distinct(sex)
) %>%
ungroup() %>%
filter(n_sex == 2) %>%
select(-n_sex) %>%
arrange(production_center, strain_name, population, sex)
}create_meta_analysis_effect_sizes <- function(mydata) {
i <- seq(1, nrow(mydata), by = 2)
input <- data.frame(
n1i = mydata$n_ind[i],
n2i = mydata$n_ind[i + 1],
x1i = mydata$x_bar[i],
x2i = mydata$x_bar[i + 1],
sd1i = mydata$x_sd[i],
sd2i = mydata$x_sd[i + 1]
)
mydata[i, ] %>%
select(strain_name, production_center, trait) %>%
mutate(
effect_size_CVR = calculate_lnCVR(CMean = input$x1i, CSD = input$sd1i, CN = input$n1i, EMean = input$x2i, ESD = input$sd2i, EN = input$n2i),
sample_variance_CVR = calculate_var_lnCVR(CMean = input$x1i, CSD = input$sd1i, CN = input$n1i, EMean = input$x2i, ESD = input$sd2i, EN = input$n2i),
effect_size_VR = calculate_lnVR(CSD = input$sd1i, CN = input$n1i, ESD = input$sd2i, EN = input$n2i),
sample_variance_VR = calculate_var_lnVR(CN = input$n1i, EN = input$n2i),
effect_size_RR = calculate_lnRR(CMean = input$x1i, CSD = input$sd1i, CN = input$n1i, EMean = input$x2i, ESD = input$sd2i, EN = input$n2i),
sample_variance_RR = calculate_var_lnRR(CMean = input$x1i, CSD = input$sd1i, CN = input$n1i, EMean = input$x2i, ESD = input$sd2i, EN = input$n2i),
err = as.factor(seq_len(n()))
)
}Based on function created by A M Senior @ the University of Otago NZ 03/01/2014:
calculate_lnCVR <- function(CMean, CSD, CN, EMean, ESD, EN) {
log(ESD) - log(EMean) + 1 / (2 * (EN - 1)) - (log(CSD) - log(CMean) + 1 / (2 * (CN - 1)))
}
calculate_var_lnCVR <- function(CMean, CSD, CN, EMean, ESD, EN, Equal_E_C_Corr = T) {
if (Equal_E_C_Corr == T) {
mvcorr <- 0 # cor.test(log(c(CMean, EMean)), log(c(CSD, ESD)))$estimate old, slightly incorrect
S2 <- CSD^2 / (CN * (CMean^2)) + 1 / (2 * (CN - 1)) - 2 * mvcorr * sqrt((CSD^2 / (CN * (CMean^2))) * (1 / (2 * (CN - 1)))) + ESD^2 / (EN * (EMean^2)) + 1 / (2 * (EN - 1)) - 2 * mvcorr * sqrt((ESD^2 / (EN * (EMean^2))) * (1 / (2 * (EN - 1))))
}
else {
Cmvcorr <- cor.test(log(CMean), log(CSD))$estimate
Emvcorr <- cor.test(log(EMean), (ESD))$estimate
S2 <- CSD^2 / (CN * (CMean^2)) + 1 / (2 * (CN - 1)) - 2 * Cmvcorr * sqrt((CSD^2 / (CN * (CMean^2))) * (1 / (2 * (CN - 1)))) + ESD^2 / (EN * (EMean^2)) + 1 / (2 * (EN - 1)) - 2 * Emvcorr * sqrt((ESD^2 / (EN * (EMean^2))) * (1 / (2 * (EN - 1))))
}
S2
}
calculate_lnVR <- function(CSD, CN, ESD, EN) {
log(ESD) - log(CSD) + 1 / (2 * (EN - 1)) - 1 / (2 * (CN - 1))
}
calculate_var_lnVR <- function(CN, EN) {
1 / (2 * (EN - 1)) + 1 / (2 * (CN - 1))
}
calculate_lnRR <- function(CMean, CSD, CN, EMean, ESD, EN) {
log(EMean) - log(CMean)
}
calculate_var_lnRR <- function(CMean, CSD, CN, EMean, ESD, EN) {
CSD^2 / (CN * CMean^2) + ESD^2 / (EN * EMean^2)
}Having loaded the necessary functions, we can get started on the dataset.
We here provide the cleaned dataset, which we have saved in a folder called export, as easy starting point. However, the full dataset can be loaded and cleaned using the data cleaning function below. We created this as it much smaller than the .csv.
This step we have already done and provide a cleaned up file which is less computing intensive. However, the cvs is provided in case this is preferred to be attempted, following the steps below:
# loads the raw data, setting some default types for various columns
load_raw <- function(filename) {
read_csv(filename,
col_types = cols(
.default = col_character(),
project_id = col_character(),
id = col_character(),
parameter_id = col_character(),
age_in_days = col_integer(),
date_of_experiment = col_datetime(format = ""),
weight = col_double(),
phenotyping_center_id = col_character(),
production_center_id = col_character(),
weight_date = col_datetime(format = ""),
date_of_birth = col_datetime(format = ""),
procedure_id = col_character(),
pipeline_id = col_character(),
biological_sample_id = col_character(),
biological_model_id = col_character(),
weight_days_old = col_integer(),
datasource_id = col_character(),
experiment_id = col_character(),
data_point = col_double(),
age_in_weeks = col_integer(),
`_version_` = col_character()
)
)
}
# Apply some standard cleaning to the data
clean_raw_data <- function(mydata) {
group <- read_csv(here("data", "ParameterGrouping.csv"))
tmp <-
mydata %>%
# Filter to IMPC source (recommend by Jeremey in email to Susi on 20 Aug 2018)
filter(datasource_name == "IMPC") %>%
# standardise trait names
mutate(parameter_name = tolower(parameter_name)) %>%
# remove extreme ages
filter(age_in_days > 0 & age_in_days < 500) %>%
# remove NAs
filter(!is.na(data_point)) %>%
# subset to reasonable set of variables
# date_of_experiment: Jeremy suggested using as an indicator of batch-level effects
select(production_center, strain_name, strain_accession_id, biological_sample_id, pipeline_stable_id, procedure_group, procedure_name, sex, date_of_experiment, age_in_days, weight, parameter_name, data_point) %>%
# sort
arrange(production_center, biological_sample_id, age_in_days)
# filter to groups with > 1 centre
# **Review** - retaining merge here to retain ordering of data used in previous version
# usually i would use mutate instead of creating sperate dataset
merge(tmp,
tmp %>% group_by(parameter_name) %>%
summarise(center_per_trait = length(unique(production_center, na.rm = TRUE)))
)%>%
filter(center_per_trait >= 2) %>%
# Define population variable
mutate(population = sprintf("%s-%s", production_center, strain_name)) %>%
# add grouping variable: these were decided based on functional groups and procedures
# **Review** - retaining match here to retain ordering of data used in rpevious version
mutate(parameter_group = group$parameter[match(parameter_name, group$parameter_name)] ) %>%
# usually i would use left_join
# left_join(by="parameter_name",
# read_csv(here("data", "ParameterGrouping.csv")) %>%
# select(-id)
# ) %>%
# Assign unique IDs (per trait)
# each unique parameter_name (=trait,use trait variable) gets a unique number ('id')
# We add a new variable, where redundant traits are combined
#[note however, at this stage the dataset still contains nonsensical traits, i.e. traits that may not contain any information on variance]
mutate(id = match(parameter_name, unique(parameter_name))) %>%
as_tibble()
}
# Load raw data - save cleaned dataset as RDS for reuse
data_raw <- load_raw(here("data","dr7.0_all_control_data.csv.gz"))
dir.create("export", F, F)
data <- data_raw %>%
clean_raw_data()
saveRDS(data, "export/data_clean.rds")For analysis we load the RDS created above and other datasets:
data <- readRDS(here("export", "data_clean.rds"))
procedures <- read_csv(here("data", "procedures.csv"))Parsed with column specification:
cols(
procedure = [31mcol_character()[39m,
GroupingTerm = [31mcol_character()[39m
)Check length of different variables / sample sizes:
length(unique(data$parameter_name)) # 232 traits[1] 232length(unique(data$parameter_group)) # 161 parameter groups[1] 161length(unique(data$procedure_name)) # 26 procedure groups[1] 26length(unique(data$biological_sample_id)) # 27147 individial mice #FZ added 11-12-2019[1] 27147#number of males and females per strain per production center #FZ added 11-12-2019
data %>% group_by(production_center, strain_name) %>% count(biological_sample_id, sex) %>% count(sex) %>% print(n = Inf)NA
NACreate function for sub-setting the data to choose only one data point per individual per trait. This is a necessary step for the loop across all traits
data_subset_parameterid_individual_by_age <- function(mydata, parameter, age_min=0, age_center=100) {
tmp <- mydata %>%
filter(
age_in_days >= age_min,
id == parameter
) %>%
# take results for single individual closest to age_center
mutate(age_diff = abs(age_center - age_in_days)) %>%
group_by(biological_sample_id) %>%
filter(age_diff == min(age_diff)) %>%
select(-age_diff)# %>%
# filter(!duplicated(biological_sample_id))
# still some individuals with multiple records (because same individual appear under different procedures, so filter to one record)
j <- match(unique(tmp$biological_sample_id), tmp$biological_sample_id)
tmp[j, ]
}Loop running meta-analysis on all traits
for (t in 1:n) {
tryCatch(
{
results <- data %>%
data_subset_parameterid_individual_by_age(t) %>%
calculate_population_stats() %>%
create_meta_analysis_effect_sizes()
# lnCVR, log repsonse-ratio of the coefficient of variance
cvr <- metafor::rma.mv(yi = effect_size_CVR, V = sample_variance_CVR,
random = list(~ 1 | strain_name, ~ 1 | production_center, ~ 1 | err),
control = list(optimizer = "optim", optmethod = "Nelder-Mead",
maxit = 1000), verbose = F, data = results)
# lnVR, comparison of standard deviations
cv <- metafor::rma.mv(yi = effect_size_VR, V = sample_variance_VR,
random = list(~ 1 | strain_name, ~ 1 | production_center, ~ 1 | err),
control = list(optimizer = "optim", optmethod = "Nelder-Mead",
maxit = 1000), verbose = F, data = results)
# for means, lnRR
means <- metafor::rma.mv(yi = effect_size_RR, V = sample_variance_RR,
random = list(~ 1 | strain_name, ~ 1 | production_center, ~ 1 | err),
control = list(optimizer = "optim", optmethod = "Nelder-Mead",
maxit = 1000), verbose = F, data = results)
f <- function(x) unlist(x[c("b", "ci.lb", "ci.ub", "se")])
results_alltraits_grouping[t, 2:14] <- c(f(cvr), f(cv), f(means), means$k)
results_alltraits_grouping[t, 15] <- unique(results$trait)
},
error = function(e) {
cat("ERROR :", t, conditionMessage(e), "\n")
}
)
}
ERROR : 84 Optimizer (optim) did not achieve convergence (convergence = 10). Single-level factor(s) found in 'random' argument. Corresponding 'sigma2' value(s) fixed to 0.Single-level factor(s) found in 'random' argument. Corresponding 'sigma2' value(s) fixed to 0.Single-level factor(s) found in 'random' argument. Corresponding 'sigma2' value(s) fixed to 0.Single-level factor(s) found in 'random' argument. Corresponding 'sigma2' value(s) fixed to 0.Single-level factor(s) found in 'random' argument. Corresponding 'sigma2' value(s) fixed to 0.Single-level factor(s) found in 'random' argument. Corresponding 'sigma2' value(s) fixed to 0.Single-level factor(s) found in 'random' argument. Corresponding 'sigma2' value(s) fixed to 0.Single-level factor(s) found in 'random' argument. Corresponding 'sigma2' value(s) fixed to 0.Single-level factor(s) found in 'random' argument. Corresponding 'sigma2' value(s) fixed to 0.Single-level factor(s) found in 'random' argument. Corresponding 'sigma2' value(s) fixed to 0.Single-level factor(s) found in 'random' argument. Corresponding 'sigma2' value(s) fixed to 0.Single-level factor(s) found in 'random' argument. Corresponding 'sigma2' value(s) fixed to 0.Single-level factor(s) found in 'random' argument. Corresponding 'sigma2' value(s) fixed to 0.Single-level factor(s) found in 'random' argument. Corresponding 'sigma2' value(s) fixed to 0.Single-level factor(s) found in 'random' argument. Corresponding 'sigma2' value(s) fixed to 0.Rows with NAs omitted from model fitting.Rows with NAs omitted from model fitting.Rows with NAs omitted from model fitting.Rows with NAs omitted from model fitting.Rows with NAs omitted from model fitting.There are outcomes with non-positive sampling variances.'V' appears to be not positive definite.ERROR : 158 Optimizer (optim) did not achieve convergence (convergence = 10). Rows with NAs omitted from model fitting.ERROR : 160 NA/NaN/Inf in 'y' Rows with NAs omitted from model fitting.ERROR : 161 NA/NaN/Inf in 'y' Rows with NAs omitted from model fitting.ERROR : 162 NA/NaN/Inf in 'y' Rows with NAs omitted from model fitting.ERROR : 163 NA/NaN/Inf in 'y' Rows with NAs omitted from model fitting.ERROR : 165 NA/NaN/Inf in 'y' Rows with NAs omitted from model fitting.ERROR : 166 NA/NaN/Inf in 'y' Rows with NAs omitted from model fitting.Rows with NAs omitted from model fitting.There are outcomes with non-positive sampling variances.'V' appears to be not positive definite.Rows with NAs omitted from model fitting.ERROR : 168 NA/NaN/Inf in 'y' Single-level factor(s) found in 'random' argument. Corresponding 'sigma2' value(s) fixed to 0.Single-level factor(s) found in 'random' argument. Corresponding 'sigma2' value(s) fixed to 0.Single-level factor(s) found in 'random' argument. Corresponding 'sigma2' value(s) fixed to 0.Single-level factor(s) found in 'random' argument. Corresponding 'sigma2' value(s) fixed to 0.Single-level factor(s) found in 'random' argument. Corresponding 'sigma2' value(s) fixed to 0.Single-level factor(s) found in 'random' argument. Corresponding 'sigma2' value(s) fixed to 0.Single-level factor(s) found in 'random' argument. Corresponding 'sigma2' value(s) fixed to 0.Single-level factor(s) found in 'random' argument. Corresponding 'sigma2' value(s) fixed to 0.Single-level factor(s) found in 'random' argument. Corresponding 'sigma2' value(s) fixed to 0.Single-level factor(s) found in 'random' argument. Corresponding 'sigma2' value(s) fixed to 0.Single-level factor(s) found in 'random' argument. Corresponding 'sigma2' value(s) fixed to 0.Single-level factor(s) found in 'random' argument. Corresponding 'sigma2' value(s) fixed to 0.Single-level factor(s) found in 'random' argument. Corresponding 'sigma2' value(s) fixed to 0.Single-level factor(s) found in 'random' argument. Corresponding 'sigma2' value(s) fixed to 0.Single-level factor(s) found in 'random' argument. Corresponding 'sigma2' value(s) fixed to 0.Rows with NAs omitted from model fitting.Rows with NAs omitted from model fitting.There are outcomes with non-positive sampling variances.'V' appears to be not positive definite.Rows with NAs omitted from model fitting.Rows with NAs omitted from model fitting.There are outcomes with non-positive sampling variances.'V' appears to be not positive definite.Rows with NAs omitted from model fitting.ERROR : 231 NA/NaN/Inf in 'y' | REVIEW: The above loop gives some errors, can these be fixed? FZ: In the above function, we use ‘tryCatch’ and ‘conditionMessage’ to prevent the loop from aborting when the first error at row 84 is produced. FZ Convergence in the two listed non-converging cases can’t be achieved by sensibly tweaking (other optim etc.). FZ Since we only learn about non-convergence in the loop, it’s difficult to exclude the two traits beforehand. FZ Similarly, the 8 traits with very low variation (160, …, 231) are hard to exclude before. FZ Warnings are ok: indicating cases where variance components are set to zero during likelihood optimization. |
| ERROR : 84 Optimizer (optim) did not achieve convergence (convergence = 10). ERROR : 158 Optimizer (optim) did not achieve convergence (convergence = 10). ERROR : 160 NA/NaN/Inf in ‘y’ ERROR : 161 NA/NaN/Inf in ‘y’ ERROR : 162 NA/NaN/Inf in ‘y’ ERROR : 163 NA/NaN/Inf in ‘y’ ERROR : 165 NA/NaN/Inf in ‘y’ ERROR : 166 NA/NaN/Inf in ‘y’ ERROR : 168 NA/NaN/Inf in ‘y’ ERROR : 231 NA/NaN/Inf in ‘y’ |
| Also a bunch of warnings, are any of these a concern? |
| > warnings() Warning messages: 1: In metafor::rma.mv(yi = effect_size_CVR, V = sample_variance_CVR, … : Rows with NAs omitted from model fitting. … 13: In metafor::rma.mv(yi = effect_size_RR, V = sample_variance_RR, … : There are outcomes with non-positive sampling variances. 14: In metafor::rma.mv(yi = effect_size_RR, V = sample_variance_RR, … : ‘V’ appears to be not positive definite. 16: In metafor::rma.mv(yi = effect_size_CVR, V = sample_variance_CVR, … : Single-level factor(s) found in ‘random’ argument. Corresponding ‘sigma2’ value(s) fixed to 0. … 50: In metafor::rma.mv(yi = effect_size_RR, V = sample_variance_RR, … : ‘V’ appears to be not positive definite |
Now that we have a “results” table with each of the meta-analytic means for all effect sizes of interest, we can use this table as part of the Shiny App, which will then be able to back calculate the percentage differences between males and females for mean, variance and coefficient of variance. We’ll export and use this in the Shiny App. Note that I have not dealt with convergence issues in some of these models, and so, this will need to be done down the road
(Note Susi 31/7/2019: This dataset contains dublicated values, plus no info on what the “traits” mean. I will change Dan N’s to one further belwo, that have been cleaned up already FILE TO USE: METACOMBO (around line 500))
Procedure names, grouping variables etc. are merged back together with the results from the metafor analysis above. This requires loading of another excel sheet, “procedures.csv”
n
[1] 232Removal of traits that did not achieve convergence, are nonsensical for analysis of variance (such as traits that show variation, such as number of ribs, digits, etc). 14 traits from the originally 232 that had been included are removed.
Review: How did we determine this the ones with problems? FZ: In addition to the sentence one line above, to do: add information about cause of exclusion ( 1. non-convergence of metafor models, or 2. no variation/nonsensical); reference traits to be excluded by trait name (not id number) FZ: excluded because of non-convergence: 84, 158 FZ: excluded because no variation/nonsensical: 144, 158, 160,…
results_alltraits_grouping2 <-
results_alltraits_grouping %>%
left_join(by="id",
data %>% select(id, parameter_group, procedure = procedure_name, procedure_name) %>% #susi: check parateer group
# REVIEW -- this bext line replciates precious code, but removes some procedures, is that right?
# FZ: No. This creates the data from the complete data set ('data'), which was not carried over into 'results_alltraits_grouping'
# FZ: We filter duplicated id's to get only one unique row per id (and there is one id per parameter_name)
filter(!duplicated(id))
) %>%
# FZ: Below we add 'procedure' (from the previously loaded 'procedures.csv') as a variable
left_join(by="procedure",
procedures %>% distinct()
)
n <- length(unique(results_alltraits_grouping2$parameter_name)) # 232Unknown or uninitialised column: 'parameter_name'.
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Error: attempt to use zero-length variable name
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Reveiw: check against old script – identical, remove once fixed
meta_clean.test <- readRDS("../meta_clean.test.rds") #FZ comment: doesn't work for me. '../' is for the github location?
all.equal(meta_clean, meta_clean.test)
all.equal(meta_clean %>% select(-parameter_group), meta_clean.test %>% mutate(id=as.integer(id), GroupingTerm = as.character(GroupingTerm)))This is the full result dataset
kable(cbind(metacombo, metacombo)) %>%
kable_styling() %>%
scroll_box(width = "100%", height = "200px")Nesting, calculating the number of parameters within each grouping term, and running the meta-analysis
metacombo_final <- metacombo %>%
group_by(GroupingTerm) %>%
#FZ comment: changed 'nest' to 'nest_legacy' to keep old syntax/functionality
nest_legacy()
# **calculate number of parameters per grouping term
metacombo_final <- metacombo_final %>% mutate(para_per_GroupingTerm = map_dbl(data, nrow))
# For all grouping terms
metacombo_final_all <- metacombo %>%
#FZ comment: changed 'nest' to 'nest_legacy' to keep old syntax/functionality
nest_legacy()
# **Final fixed effects meta-analyses within grouping terms, with SE of the estimate
overall1 <- metacombo_final %>%
mutate(
model_lnCVR = map(data, ~ metafor::rma.uni(
yi = .x$lnCVR, sei = (.x$lnCVR_upper - .x$lnCVR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
)),
model_lnVR = map(data, ~ metafor::rma.uni(
yi = .x$lnVR, sei = (.x$lnVR_upper - .x$lnVR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
)),
model_lnRR = map(data, ~ metafor::rma.uni(
yi = .x$lnRR, sei = (.x$lnRR_upper - .x$lnRR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
))
)
# **Final fixed effects meta-analyses ACROSS grouping terms, with SE of the estimate
overall_all1 <- metacombo_final_all %>%
mutate(
model_lnCVR = map(data, ~ metafor::rma.uni(
yi = .x$lnCVR, sei = (.x$lnCVR_upper - .x$lnCVR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
)),
model_lnVR = map(data, ~ metafor::rma.uni(
yi = .x$lnVR, sei = (.x$lnVR_upper - .x$lnVR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
)),
model_lnRR = map(data, ~ metafor::rma.uni(
yi = .x$lnRR, sei = (.x$lnRR_upper - .x$lnRR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
))
)Re-structure data for each grouping term; delete unused variables #FZ comment: referencing of cells below doesn’t depend on previous oreding of the data, i.e. only changes if output structure from metafor::rma.uni changes
Behaviour <- as.data.frame(overall1 %>% filter(., GroupingTerm == "Behaviour") %>% mutate(
lnCVR = .[[4]][[1]]$b, lnCVR_lower = .[[4]][[1]]$ci.lb, lnCVR_upper = .[[4]][[1]]$ci.ub, lnCVR_se = .[[4]][[1]]$se,
lnVR = .[[5]][[1]]$b, lnVR_lower = .[[5]][[1]]$ci.lb, lnVR_upper = .[[5]][[1]]$ci.ub, lnVR_se = .[[5]][[1]]$se,
lnRR = .[[6]][[1]]$b, lnRR_lower = .[[6]][[1]]$ci.lb, lnRR_upper = .[[6]][[1]]$ci.ub, lnRR_se = .[[6]][[1]]$se
))[, c(1, 7:18)]
Immunology <- as.data.frame(overall1 %>% filter(., GroupingTerm == "Immunology") %>% mutate(
lnCVR = .[[4]][[1]]$b, lnCVR_lower = .[[4]][[1]]$ci.lb, lnCVR_upper = .[[4]][[1]]$ci.ub, lnCVR_se = .[[4]][[1]]$se,
lnVR = .[[5]][[1]]$b, lnVR_lower = .[[5]][[1]]$ci.lb, lnVR_upper = .[[5]][[1]]$ci.ub, lnVR_se = .[[5]][[1]]$se,
lnRR = .[[6]][[1]]$b, lnRR_lower = .[[6]][[1]]$ci.lb, lnRR_upper = .[[6]][[1]]$ci.ub, lnRR_se = .[[6]][[1]]$se
))[, c(1, 7:18)]
Hematology <- as.data.frame(overall1 %>% filter(., GroupingTerm == "Hematology") %>% mutate(
lnCVR = .[[4]][[1]]$b, lnCVR_lower = .[[4]][[1]]$ci.lb, lnCVR_upper = .[[4]][[1]]$ci.ub, lnCVR_se = .[[4]][[1]]$se,
lnVR = .[[5]][[1]]$b, lnVR_lower = .[[5]][[1]]$ci.lb, lnVR_upper = .[[5]][[1]]$ci.ub, lnVR_se = .[[5]][[1]]$se,
lnRR = .[[6]][[1]]$b, lnRR_lower = .[[6]][[1]]$ci.lb, lnRR_upper = .[[6]][[1]]$ci.ub, lnRR_se = .[[6]][[1]]$se
))[, c(1, 7:18)]
Hearing <- as.data.frame(overall1 %>% filter(., GroupingTerm == "Hearing") %>% mutate(
lnCVR = .[[4]][[1]]$b, lnCVR_lower = .[[4]][[1]]$ci.lb, lnCVR_upper = .[[4]][[1]]$ci.ub, lnCVR_se = .[[4]][[1]]$se,
lnVR = .[[5]][[1]]$b, lnVR_lower = .[[5]][[1]]$ci.lb, lnVR_upper = .[[5]][[1]]$ci.ub, lnVR_se = .[[5]][[1]]$se,
lnRR = .[[6]][[1]]$b, lnRR_lower = .[[6]][[1]]$ci.lb, lnRR_upper = .[[6]][[1]]$ci.ub, lnRR_se = .[[6]][[1]]$se
))[, c(1, 7:18)]
Physiology <- as.data.frame(overall1 %>% filter(., GroupingTerm == "Physiology") %>% mutate(
lnCVR = .[[4]][[1]]$b, lnCVR_lower = .[[4]][[1]]$ci.lb, lnCVR_upper = .[[4]][[1]]$ci.ub, lnCVR_se = .[[4]][[1]]$se,
lnVR = .[[5]][[1]]$b, lnVR_lower = .[[5]][[1]]$ci.lb, lnVR_upper = .[[5]][[1]]$ci.ub, lnVR_se = .[[5]][[1]]$se,
lnRR = .[[6]][[1]]$b, lnRR_lower = .[[6]][[1]]$ci.lb, lnRR_upper = .[[6]][[1]]$ci.ub, lnRR_se = .[[6]][[1]]$se
))[, c(1, 7:18)]
Metabolism <- as.data.frame(overall1 %>% filter(., GroupingTerm == "Metabolism") %>% mutate(
lnCVR = .[[4]][[1]]$b, lnCVR_lower = .[[4]][[1]]$ci.lb, lnCVR_upper = .[[4]][[1]]$ci.ub, lnCVR_se = .[[4]][[1]]$se,
lnVR = .[[5]][[1]]$b, lnVR_lower = .[[5]][[1]]$ci.lb, lnVR_upper = .[[5]][[1]]$ci.ub, lnVR_se = .[[5]][[1]]$se,
lnRR = .[[6]][[1]]$b, lnRR_lower = .[[6]][[1]]$ci.lb, lnRR_upper = .[[6]][[1]]$ci.ub, lnRR_se = .[[6]][[1]]$se
))[, c(1, 7:18)]
Morphology <- as.data.frame(overall1 %>% filter(., GroupingTerm == "Morphology") %>% mutate(
lnCVR = .[[4]][[1]]$b, lnCVR_lower = .[[4]][[1]]$ci.lb, lnCVR_upper = .[[4]][[1]]$ci.ub, lnCVR_se = .[[4]][[1]]$se,
lnVR = .[[5]][[1]]$b, lnVR_lower = .[[5]][[1]]$ci.lb, lnVR_upper = .[[5]][[1]]$ci.ub, lnVR_se = .[[5]][[1]]$se,
lnRR = .[[6]][[1]]$b, lnRR_lower = .[[6]][[1]]$ci.lb, lnRR_upper = .[[6]][[1]]$ci.ub, lnRR_se = .[[6]][[1]]$se
))[, c(1, 7:18)]
Heart <- as.data.frame(overall1 %>% filter(., GroupingTerm == "Heart") %>% mutate(
lnCVR = .[[4]][[1]]$b, lnCVR_lower = .[[4]][[1]]$ci.lb, lnCVR_upper = .[[4]][[1]]$ci.ub, lnCVR_se = .[[4]][[1]]$se,
lnVR = .[[5]][[1]]$b, lnVR_lower = .[[5]][[1]]$ci.lb, lnVR_upper = .[[5]][[1]]$ci.ub, lnVR_se = .[[5]][[1]]$se,
lnRR = .[[6]][[1]]$b, lnRR_lower = .[[6]][[1]]$ci.lb, lnRR_upper = .[[6]][[1]]$ci.ub, lnRR_se = .[[6]][[1]]$se
))[, c(1, 7:18)]
Eye <- as.data.frame(overall1 %>% filter(., GroupingTerm == "Eye") %>% mutate(
lnCVR = .[[4]][[1]]$b, lnCVR_lower = .[[4]][[1]]$ci.lb, lnCVR_upper = .[[4]][[1]]$ci.ub, lnCVR_se = .[[4]][[1]]$se,
lnVR = .[[5]][[1]]$b, lnVR_lower = .[[5]][[1]]$ci.lb, lnVR_upper = .[[5]][[1]]$ci.ub, lnVR_se = .[[5]][[1]]$se,
lnRR = .[[6]][[1]]$b, lnRR_lower = .[[6]][[1]]$ci.lb, lnRR_upper = .[[6]][[1]]$ci.ub, lnRR_se = .[[6]][[1]]$se
))[, c(1, 7:18)]
All <- as.data.frame(overall_all1 %>% mutate(
lnCVR = .[[2]][[1]]$b, lnCVR_lower = .[[2]][[1]]$ci.lb, lnCVR_upper = .[[2]][[1]]$ci.ub, lnCVR_se = .[[2]][[1]]$se, lnVR = .[[3]][[1]]$b, lnVR_lower = .[[3]][[1]]$ci.lb, lnVR_upper = .[[3]][[1]]$ci.ub, lnVR_se = .[[3]][[1]]$se,
lnRR = .[[4]][[1]]$b, lnRR_lower = .[[4]][[1]]$ci.lb, lnRR_upper = .[[4]][[1]]$ci.ub, lnRR_se = .[[4]][[1]]$se
))[, c(5:16)]
All$lnCVR <- as.numeric(All$lnCVR)
All$lnVR <- as.numeric(All$lnVR)
All$lnRR <- as.numeric(All$lnRR)
All <- All %>% mutate(GroupingTerm = "All")
overall2 <- bind_rows(Behaviour, Morphology, Metabolism, Physiology, Immunology, Hematology, Heart, Hearing, Eye, All) #FZ: warnings are okRe-order grouping terms
meta_clean$GroupingTerm <- factor(meta_clean$GroupingTerm, levels = c("Behaviour", "Morphology", "Metabolism", "Physiology", "Immunology", "Hematology", "Heart", "Hearing", "Eye"))
meta_clean$GroupingTerm <- factor(meta_clean$GroupingTerm, rev(levels(meta_clean$GroupingTerm)))
# *Prepare data for all traits
meta.plot2.all <- meta_clean %>%
select(lnCVR, lnVR, lnRR, GroupingTerm) %>%
arrange(GroupingTerm)
meta.plot2.all.b <- gather(meta.plot2.all, trait, value, c(lnCVR, lnRR)) # lnVR,
meta.plot2.all.b$trait <- factor(meta.plot2.all.b$trait, levels = c("lnCVR", "lnRR")) # "lnVR",
meta.plot2.all.c <- meta.plot2.all.b %>%
group_by_at(vars(trait, GroupingTerm)) %>%
summarise(
malebias = sum(value > 0), femalebias = sum(value <= 0), total = malebias + femalebias,
malepercent = malebias * 100 / total, femalepercent = femalebias * 100 / total
)
meta.plot2.all.c$label <- "All traits"
# restructure to create stacked bar plots
meta.plot2.all.d <- as.data.frame(meta.plot2.all.c)
meta.plot2.all.e <- gather(meta.plot2.all.d, key = sex, value = percent, malepercent:femalepercent, factor_key = TRUE)
# create new sample size variable
meta.plot2.all.e$samplesize <- with(meta.plot2.all.e, ifelse(sex == "malepercent", malebias, femalebias))
# add summary row ('All') and re-arrange rows into correct order for plotting #FZ added
meta.plot2.all.f <- meta.plot2.all.e %>% group_by(trait, sex) %>%
summarise(GroupingTerm = "All", malebias = sum(malebias), femalebias = sum(femalebias), total = malebias + femalebias,
label = "All traits", samplesize = sum(samplesize)) %>%
mutate(percent = ifelse(sex == "femalepercent", femalebias*100/(malebias+femalebias), malebias*100/(malebias+femalebias))) %>%
bind_rows(meta.plot2.all.e, .) %>%
mutate(rownumber = row_number()) %>%
.[c(37, 1:9, 39, 10:18, 38, 19:27, 40, 28:36), ]
meta.plot2.all.f$GroupingTerm <- factor(meta.plot2.all.f$GroupingTerm, levels = c("Behaviour", "Morphology", "Metabolism", "Physiology", "Immunology", "Hematology", "Heart", "Hearing", "Eye", "All"))
meta.plot2.all.f$GroupingTerm <- factor(meta.plot2.all.f$GroupingTerm, rev(levels(meta.plot2.all.f$GroupingTerm)))
malebias_Fig2_alltraits <-
ggplot(meta.plot2.all.f) +
aes(x = GroupingTerm, y = percent, fill = sex) +
geom_col() +
geom_hline(yintercept = 50, linetype = "dashed", color = "gray40") +
geom_text(
data = subset(meta.plot2.all.f, samplesize != 0), aes(label = samplesize), position = position_stack(vjust = .5),
color = "white", size = 3.5
) +
facet_grid(
cols = vars(trait), rows = vars(label), labeller = label_wrap_gen(width = 18),
scales = "free", space = "free"
) +
scale_fill_brewer(palette = "Set2") +
theme_bw(base_size = 18) +
theme(
strip.text.y = element_text(angle = 270, size = 10, margin = margin(t = 15, r = 15, b = 15, l = 15)),
strip.text.x = element_text(size = 12),
strip.background = element_rect(colour = NULL, linetype = "blank", fill = "gray90"),
text = element_text(size = 14),
panel.spacing = unit(0.5, "lines"),
panel.border = element_blank(),
axis.line = element_line(),
panel.grid.major.x = element_line(linetype = "solid", colour = "gray95"),
panel.grid.major.y = element_line(linetype = "solid", color = "gray95"),
panel.grid.minor.y = element_blank(),
panel.grid.minor.x = element_blank(),
legend.position = "none",
axis.title.x = element_blank(),
axis.title.y = element_blank()
) +
coord_flip()
# malebias_Fig2_alltraits #(panel A in Figure 4 in ms)create column with 1= different from zero, 0= zero included in CI
meta.plot2.sig <- meta_clean %>%
mutate(
lnCVRsig = ifelse(lnCVR_lower * lnCVR_upper > 0, 1, 0), lnVRsig = ifelse(lnVR_lower * lnVR_upper > 0, 1, 0),
lnRRsig = ifelse(lnRR_lower * lnRR_upper > 0, 1, 0)
)
meta.plot2.sig.b <- meta.plot2.sig[, c("lnCVR", "lnRR", "lnCVRsig", "lnVRsig", "lnRRsig", "GroupingTerm")] # "lnVR",
meta.plot2.sig.c <- gather(meta.plot2.sig.b, trait, value, lnCVR:lnRR)
meta.plot2.sig.c$sig <- "placeholder"
meta.plot2.sig.c$trait <- factor(meta.plot2.sig.c$trait, levels = c("lnCVR", "lnRR")) # "lnVR",
meta.plot2.sig.c$sig <- ifelse(meta.plot2.sig.c$trait == "lnCVR", meta.plot2.sig.c$lnCVRsig,
ifelse(meta.plot2.sig.c$trait == "lnVR", meta.plot2.sig.c$lnVRsig, meta.plot2.sig.c$lnRRsig)
)
# choosing sex biased ln-ratios significantly larger than 0
meta.plot2.sig.malebias <- meta.plot2.sig.c %>%
group_by_at(vars(trait, GroupingTerm)) %>%
filter(sig == 1) %>%
summarise(male_sig = sum(value > 0), female_sig = sum(value < 0), total = male_sig + female_sig)
meta.plot2.sig.malebias <- ungroup(meta.plot2.sig.malebias) %>%
add_row(trait = "lnCVR", GroupingTerm = "Hearing", male_sig = 0, female_sig = 0, .before = 4) %>% # add "Hearing" for lnCVR (not filtered as only zeros)
mutate(malepercent = male_sig * 100 / total, femalepercent = female_sig * 100 / total)
meta.plot2.sig.malebias$label <- "CI not overlapping zero"
# restructure to create stacked bar plots
meta.plot2.sig.bothsexes <- as.data.frame(meta.plot2.sig.malebias)
meta.plot2.sig.bothsexes.b <- gather(meta.plot2.sig.bothsexes, key = sex, value = percent, malepercent:femalepercent, factor_key = TRUE)
# create new sample size variable
meta.plot2.sig.bothsexes.b$samplesize <- with(meta.plot2.sig.bothsexes.b, ifelse(sex == "malepercent", male_sig, female_sig))
# *Plot Fig2 all significant results (CI not overlapping zero):
# no sig. lnCVR for 'Hearing' in either sex; no sig. male-biased lnCVR for 'Immunology' and 'Eye, and no sig. male-biased lnVR for 'Eye'
malebias_Fig2_sigtraits <-
ggplot(meta.plot2.sig.bothsexes.b) +
aes(x = GroupingTerm, y = percent, fill = sex) +
geom_col() +
geom_hline(yintercept = 50, linetype = "dashed", color = "gray40") +
geom_text(
data = subset(meta.plot2.sig.bothsexes.b, samplesize != 0), aes(label = samplesize), position = position_stack(vjust = .5),
color = "white", size = 3.5
) +
facet_grid(
cols = vars(trait), rows = vars(label), labeller = label_wrap_gen(width = 18),
scales = "free", space = "free"
) +
scale_fill_brewer(palette = "Set2") +
theme_bw(base_size = 18) +
theme(
strip.text.y = element_text(angle = 270, size = 10, margin = margin(t = 15, r = 15, b = 15, l = 15)),
strip.text.x = element_text(size = 12),
strip.background = element_rect(colour = NULL, linetype = "blank", fill = "gray90"),
text = element_text(size = 14),
panel.spacing = unit(0.5, "lines"),
panel.border = element_blank(),
axis.line = element_line(),
panel.grid.major.x = element_line(linetype = "solid", colour = "gray95"),
panel.grid.major.y = element_line(linetype = "solid", color = "gray95"),
panel.grid.minor.y = element_blank(),
panel.grid.minor.x = element_blank(),
legend.position = "none",
axis.title.x = element_blank(),
axis.title.y = element_blank()
) +
coord_flip()Prepare data for traits with effect size ratios > 10% larger in males
meta.plot2.over10 <- meta_clean %>%
select(lnCVR, lnRR, GroupingTerm) %>%
arrange(GroupingTerm) # lnVR,
meta.plot2.over10.b <- gather(meta.plot2.over10, trait, value, c(lnCVR, lnRR)) # lnVR,
meta.plot2.over10.b$trait <- factor(meta.plot2.over10.b$trait, levels = c("lnCVR", "lnRR")) # "lnVR",
meta.plot2.over10.c <- meta.plot2.over10.b %>%
group_by_at(vars(trait, GroupingTerm)) %>%
summarise(
malebias = sum(value > log(11 / 10)), femalebias = sum(value < log(9 / 10)), total = malebias + femalebias,
malepercent = malebias * 100 / total, femalepercent = femalebias * 100 / total
)
meta.plot2.over10.c$label <- "Sex difference in m/f ratios > 10%"
# restructure to create stacked bar plots
meta.plot2.over10.c <- as.data.frame(meta.plot2.over10.c)
meta.plot2.over10.d <- gather(meta.plot2.over10.c, key = sex, value = percent, malepercent:femalepercent, factor_key = TRUE)
# create new sample size variable
meta.plot2.over10.d$samplesize <- with(meta.plot2.over10.d, ifelse(sex == "malepercent", malebias, femalebias))
# *Plot Fig2 Sex difference in m/f ratio > 10%
malebias_Fig2_over10 <-
ggplot(meta.plot2.over10.d) +
aes(x = GroupingTerm, y = percent, fill = sex) +
geom_col() +
geom_hline(yintercept = 50, linetype = "dashed", color = "gray40") +
geom_text(
data = subset(meta.plot2.over10.d, samplesize != 0), aes(label = samplesize), position = position_stack(vjust = .5),
color = "white", size = 3.5
) +
facet_grid(
cols = vars(trait), rows = vars(label), labeller = label_wrap_gen(width = 18),
scales = "free", space = "free"
) +
scale_fill_brewer(palette = "Set2") +
theme_bw(base_size = 18) +
theme(
strip.text.y = element_text(angle = 270, size = 10, margin = margin(t = 15, r = 15, b = 15, l = 15)),
strip.text.x = element_blank(),
strip.background = element_rect(colour = NULL, linetype = "blank", fill = "gray90"),
text = element_text(size = 14),
panel.spacing = unit(0.5, "lines"),
panel.border = element_blank(),
axis.line = element_line(),
panel.grid.major.x = element_line(linetype = "solid", colour = "gray95"),
panel.grid.major.y = element_line(linetype = "solid", color = "gray95"),
panel.grid.minor.y = element_blank(),
panel.grid.minor.x = element_blank(),
legend.position = "none",
axis.title.x = element_blank(),
axis.title.y = element_blank()
) +
coord_flip()
# malebias_Fig2_over10 (Panel C in Fig 5 in ms)Data are restructured, and grouping terms are being re-ordered
overall3 <- gather(overall2, parameter, value, c(lnCVR, lnRR), factor_key = TRUE) # lnVR,
lnCVR.ci <- overall3 %>%
filter(parameter == "lnCVR") %>%
mutate(ci.low = lnCVR_lower, ci.high = lnCVR_upper)
lnVR.ci <- overall3 %>%
filter(parameter == "lnVR") %>%
mutate(ci.low = lnVR_lower, ci.high = lnVR_upper)
lnRR.ci <- overall3 %>%
filter(parameter == "lnRR") %>%
mutate(ci.low = lnRR_lower, ci.high = lnRR_upper)
overall4 <- bind_rows(lnCVR.ci, lnRR.ci) %>% select(GroupingTerm, parameter, value, ci.low, ci.high) # lnVR.ci,
# re-order Grouping Terms
overall4$GroupingTerm <- factor(overall4$GroupingTerm, levels = c("Behaviour", "Morphology", "Metabolism", "Physiology", "Immunology", "Hematology", "Heart", "Hearing", "Eye", "All"))
overall4$GroupingTerm <- factor(overall4$GroupingTerm, rev(levels(overall4$GroupingTerm)))
overall4$label <- "All traits"
kable(cbind(overall4, overall4)) %>%
kable_styling() %>%
scroll_box(width = "100%", height = "200px")Preparation: Sub-Plot for Figure 3: all traits (4B)
Metameta_Fig3_alltraits <- overall4 %>%
ggplot(aes(y = GroupingTerm, x = value)) +
geom_errorbarh(aes(
xmin = ci.low,
xmax = ci.high
),
height = 0.1, show.legend = FALSE
) +
geom_point(aes(shape = parameter),
fill = "black",
color = "black", size = 2.2,
show.legend = FALSE
) +
scale_x_continuous(
limits = c(-0.24, 0.25),
breaks = c(-0.2, -0.1, 0, 0.1, 0.2),
name = "Effect size"
) +
geom_vline(
xintercept = 0,
color = "black",
linetype = "dashed"
) +
facet_grid(
cols = vars(parameter), rows = vars(label),
labeller = label_wrap_gen(width = 23),
scales = "free",
space = "free"
) +
theme_bw() +
theme(
strip.text.y = element_text(angle = 270, size = 10, margin = margin(t = 15, r = 15, b = 15, l = 15)),
strip.text.x = element_text(size = 12),
strip.background = element_rect(colour = NULL, linetype = "blank", fill = "gray90"),
text = element_text(size = 14),
panel.spacing = unit(0.5, "lines"),
panel.border = element_blank(),
axis.line = element_line(),
panel.grid.major.x = element_line(linetype = "solid", colour = "gray95"),
panel.grid.major.y = element_line(linetype = "solid", color = "gray95"),
panel.grid.minor.y = element_blank(),
panel.grid.minor.x = element_blank(),
legend.title = element_blank(),
axis.title.x = element_text(hjust = 0.5, size = 14),
axis.title.y = element_blank()
)
# Metameta_Fig3_alltraitsPrepare data create column with 1= different from zero, 0= zero included in CI Male-biased (significant) traits
meta.male.plot3.sig <- metacombo %>%
mutate(
sigCVR = ifelse(lnCVR_lower > 0, 1, 0),
sigVR = ifelse(lnVR_lower > 0, 1, 0),
sigRR = ifelse(lnRR_lower > 0, 1, 0)
)
# Significant subset for lnCVR
metacombo_male.plot3.CVR <- meta.male.plot3.sig %>%
filter(sigCVR == 1) %>%
group_by(GroupingTerm) %>%
nest()
metacombo_male.plot3.CVR.all <- meta.male.plot3.sig %>%
filter(sigCVR == 1) %>%
nest()
# Significant subset for lnVR
metacombo_male.plot3.VR <- meta.male.plot3.sig %>%
filter(sigVR == 1) %>%
group_by(GroupingTerm) %>%
nest()
metacombo_male.plot3.VR.all <- meta.male.plot3.sig %>%
filter(sigVR == 1) %>%
nest()
# Significant subset for lnRR
metacombo_male.plot3.RR <- meta.male.plot3.sig %>%
filter(sigRR == 1) %>%
group_by(GroupingTerm) %>%
nest()
metacombo_male.plot3.RR.all <- meta.male.plot3.sig %>%
filter(sigRR == 1) %>%
nest()
# **Final fixed effects meta-analyses within grouping terms, with SE of the estimate
plot3.male.meta.CVR <- metacombo_male.plot3.CVR %>%
mutate(model_lnCVR = map(data, ~ metafor::rma.uni(
yi = .x$lnCVR, sei = (.x$lnCVR_upper - .x$lnCVR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
)))
plot3.male.meta.VR <- metacombo_male.plot3.VR %>%
mutate(model_lnVR = map(data, ~ metafor::rma.uni(
yi = .x$lnVR, sei = (.x$lnVR_upper - .x$lnVR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
)))
plot3.male.meta.RR <- metacombo_male.plot3.RR %>%
mutate(model_lnRR = map(data, ~ metafor::rma.uni(
yi = .x$lnRR, sei = (.x$lnRR_upper - .x$lnRR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
)))
# Across all grouping terms #
plot3.male.meta.CVR.all <- metacombo_male.plot3.CVR.all %>%
mutate(model_lnCVR = map(data, ~ metafor::rma.uni(
yi = .x$lnCVR, sei = (.x$lnCVR_upper - .x$lnCVR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
)))
plot3.male.meta.CVR.all <- plot3.male.meta.CVR.all %>% mutate(GroupingTerm = "All")
plot3.male.meta.VR.all <- metacombo_male.plot3.VR.all %>%
mutate(model_lnVR = map(data, ~ metafor::rma.uni(
yi = .x$lnVR, sei = (.x$lnVR_upper - .x$lnVR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
)))
plot3.male.meta.VR.all <- plot3.male.meta.VR.all %>% mutate(GroupingTerm = "All")
plot3.male.meta.RR.all <- metacombo_male.plot3.RR.all %>%
mutate(model_lnRR = map(data, ~ metafor::rma.uni(
yi = .x$lnRR, sei = (.x$lnRR_upper - .x$lnRR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
)))
plot3.male.meta.RR.all <- plot3.male.meta.RR.all %>% mutate(GroupingTerm = "All")
# Combine with separate grouping term results
plot3.male.meta.CVR <- bind_rows(plot3.male.meta.CVR, plot3.male.meta.CVR.all)
plot3.male.meta.VR <- bind_rows(plot3.male.meta.VR, plot3.male.meta.VR.all)
plot3.male.meta.RR <- bind_rows(plot3.male.meta.RR, plot3.male.meta.RR.all)
# **Re-structure data for each grouping term; delete un-used variables
plot3.male.meta.CVR.b <- as.data.frame(plot3.male.meta.CVR %>% group_by(GroupingTerm) %>%
mutate(
lnCVR = map_dbl(model_lnCVR, pluck(2)), lnCVR_lower = map_dbl(model_lnCVR, pluck(6)),
lnCVR_upper = map_dbl(model_lnCVR, pluck(7)), lnCVR_se = map_dbl(model_lnCVR, pluck(3))
))[, c(1, 4:7)]
add.row.hearing <- as.data.frame(t(c("Hearing", NA, NA, NA, NA))) %>% setNames(names(plot3.male.meta.CVR.b))
plot3.male.meta.CVR.b <- bind_rows(plot3.male.meta.CVR.b, add.row.hearing)
plot3.male.meta.CVR.b <- plot3.male.meta.CVR.b[order(plot3.male.meta.CVR.b$GroupingTerm), ]
plot3.male.meta.VR.b <- as.data.frame(plot3.male.meta.VR %>% group_by(GroupingTerm) %>%
mutate(
lnVR = map_dbl(model_lnVR, pluck(2)), lnVR_lower = map_dbl(model_lnVR, pluck(6)),
lnVR_upper = map_dbl(model_lnVR, pluck(7)), lnVR_se = map_dbl(model_lnVR, pluck(3))
))[, c(1, 4:7)]
plot3.male.meta.VR.b <- plot3.male.meta.VR.b[order(plot3.male.meta.VR.b$GroupingTerm), ]
plot3.male.meta.RR.b <- as.data.frame(plot3.male.meta.RR %>% group_by(GroupingTerm) %>%
mutate(
lnRR = map_dbl(model_lnRR, pluck(2)), lnRR_lower = map_dbl(model_lnRR, pluck(6)),
lnRR_upper = map_dbl(model_lnRR, pluck(7)), lnRR_se = map_dbl(model_lnRR, pluck(3))
))[, c(1, 4:7)]
plot3.male.meta.RR.b <- plot3.male.meta.RR.b[order(plot3.male.meta.RR.b$GroupingTerm), ]
overall.male.plot3 <- full_join(plot3.male.meta.CVR.b, plot3.male.meta.VR.b)
overall.male.plot3 <- full_join(overall.male.plot3, plot3.male.meta.RR.b)
overall.male.plot3$GroupingTerm <- factor(overall.male.plot3$GroupingTerm, levels = c("Behaviour", "Morphology", "Metabolism", "Physiology", "Immunology", "Hematology", "Heart", "Hearing", "Eye", "All"))
overall.male.plot3$GroupingTerm <- factor(overall.male.plot3$GroupingTerm, rev(levels(overall.male.plot3$GroupingTerm)))
# add missing GroupingTerms for plot
overall.male.plot3 <- add_row(overall.male.plot3, GroupingTerm = "Behaviour")
overall.male.plot3 <- add_row(overall.male.plot3, GroupingTerm = "Immunology")
overall.male.plot3 <- add_row(overall.male.plot3, GroupingTerm = "Eye")
overall.male.plot3$GroupingTerm <- factor(overall.male.plot3$GroupingTerm, levels = c("Behaviour", "Morphology", "Metabolism", "Physiology", "Immunology", "Hematology", "Heart", "Hearing", "Eye", "All"))
overall.male.plot3$GroupingTerm <- factor(overall.male.plot3$GroupingTerm, rev(levels(overall.male.plot3$GroupingTerm)))
# str(overall.male.plot3)Restructure MALE data for plotting
overall3.male.sig <- gather(overall.male.plot3, parameter, value, c(lnCVR, lnRR), factor_key = TRUE) # lnVR,
lnCVR.ci <- overall3.male.sig %>%
filter(parameter == "lnCVR") %>%
mutate(ci.low = lnCVR_lower, ci.high = lnCVR_upper)
# lnVR.ci <- overall3.male.sig %>% filter(parameter == "lnVR") %>% mutate(ci.low = lnVR_lower, ci.high = lnVR_upper)
lnRR.ci <- overall3.male.sig %>%
filter(parameter == "lnRR") %>%
mutate(ci.low = lnRR_lower, ci.high = lnRR_upper)
overall4.male.sig <- bind_rows(lnCVR.ci, lnRR.ci) %>% select(GroupingTerm, parameter, value, ci.low, ci.high) # lnVR.ci,
overall4.male.sig$label <- "CI not overlapping zero"Plot Fig5b all significant results (CI not overlapping zero) for males
Metameta_Fig3_male.sig <- overall4.male.sig %>%
ggplot(aes(y = GroupingTerm, x = value)) +
geom_errorbarh(aes(
xmin = ci.low,
xmax = ci.high
),
height = 0.1, show.legend = FALSE
) +
geom_point(aes(shape = parameter),
fill = "mediumaquamarine", color = "mediumaquamarine", size = 2.2,
show.legend = FALSE
) +
scale_x_continuous(
limits = c(0, 0.4),
breaks = c(0, 0.3),
name = "Effect size"
) +
geom_vline(
xintercept = 0,
color = "black",
linetype = "dashed"
) +
facet_grid(
cols = vars(parameter), rows = vars(label),
labeller = label_wrap_gen(width = 23),
scales = "free",
space = "free"
) +
theme_bw() +
theme(
strip.text.y = element_text(angle = 270, size = 10, margin = margin(t = 15, r = 15, b = 15, l = 15)),
strip.text.x = element_text(size = 12),
strip.background = element_rect(colour = NULL, linetype = "blank", fill = "gray90"),
text = element_text(size = 14),
panel.spacing = unit(0.5, "lines"),
panel.border = element_blank(),
axis.line = element_line(),
panel.grid.major.x = element_line(linetype = "solid", colour = "gray95"),
panel.grid.major.y = element_line(linetype = "solid", color = "gray95"),
panel.grid.minor.y = element_blank(),
panel.grid.minor.x = element_blank(),
legend.title = element_blank(),
axis.title.x = element_blank(),
axis.title.y = element_blank()
)
# Metameta_Fig3_male.sigFemale Fig5B sig
Prepare data for traits with CI not overlapping 0 create column with 1= different from zero, 0= zero included in CI
# female-biased traits
meta.female.plot3.sig <- metacombo %>%
mutate(
sigCVR = ifelse(lnCVR_upper < 0, 1, 0),
sigVR = ifelse(lnVR_upper < 0, 1, 0),
sigRR = ifelse(lnRR_upper < 0, 1, 0)
)
# Significant subset for lnCVR
metacombo_female.plot3.CVR <- meta.female.plot3.sig %>%
filter(sigCVR == 1) %>%
group_by(GroupingTerm) %>%
nest()
metacombo_female.plot3.CVR.all <- meta.female.plot3.sig %>%
filter(sigCVR == 1) %>%
nest()
# Significant subset for lnVR
metacombo_female.plot3.VR <- meta.female.plot3.sig %>%
filter(sigVR == 1) %>%
group_by(GroupingTerm) %>%
nest()
metacombo_female.plot3.VR.all <- meta.female.plot3.sig %>%
filter(sigVR == 1) %>%
nest()
# Significant subset for lnRR
metacombo_female.plot3.RR <- meta.female.plot3.sig %>%
filter(sigRR == 1) %>%
group_by(GroupingTerm) %>%
nest()
metacombo_female.plot3.RR.all <- meta.female.plot3.sig %>%
filter(sigRR == 1) %>%
nest()
# **Final fixed effects meta-analyses within grouping terms, with SE of the estimate
plot3.female.meta.CVR <- metacombo_female.plot3.CVR %>%
mutate(model_lnCVR = map(data, ~ metafor::rma.uni(
yi = .x$lnCVR, sei = (.x$lnCVR_upper - .x$lnCVR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
)))
plot3.female.meta.VR <- metacombo_female.plot3.VR %>%
mutate(model_lnVR = map(data, ~ metafor::rma.uni(
yi = .x$lnVR, sei = (.x$lnVR_upper - .x$lnVR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
)))
plot3.female.meta.RR <- metacombo_female.plot3.RR %>%
mutate(model_lnRR = map(data, ~ metafor::rma.uni(
yi = .x$lnRR, sei = (.x$lnRR_upper - .x$lnRR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
)))
# Across all grouping terms #
plot3.female.meta.CVR.all <- metacombo_female.plot3.CVR.all %>%
mutate(model_lnCVR = map(data, ~ metafor::rma.uni(
yi = .x$lnCVR, sei = (.x$lnCVR_upper - .x$lnCVR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
)))
plot3.female.meta.CVR.all <- plot3.female.meta.CVR.all %>% mutate(GroupingTerm = "All")
plot3.female.meta.VR.all <- metacombo_female.plot3.VR.all %>%
mutate(model_lnVR = map(data, ~ metafor::rma.uni(
yi = .x$lnVR, sei = (.x$lnVR_upper - .x$lnVR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
)))
plot3.female.meta.VR.all <- plot3.female.meta.VR.all %>% mutate(GroupingTerm = "All")
plot3.female.meta.RR.all <- metacombo_female.plot3.RR.all %>%
mutate(model_lnRR = map(data, ~ metafor::rma.uni(
yi = .x$lnRR, sei = (.x$lnRR_upper - .x$lnRR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
)))
plot3.female.meta.RR.all <- plot3.female.meta.RR.all %>% mutate(GroupingTerm = "All")
# Combine with separate grouping term results
plot3.female.meta.CVR <- bind_rows(plot3.female.meta.CVR, plot3.female.meta.CVR.all)
plot3.female.meta.VR <- bind_rows(plot3.female.meta.VR, plot3.female.meta.VR.all)
plot3.female.meta.RR <- bind_rows(plot3.female.meta.RR, plot3.female.meta.RR.all)
# **Re-structure data for each grouping term; delete un-used variables
plot3.female.meta.CVR.b <- as.data.frame(plot3.female.meta.CVR %>% group_by(GroupingTerm) %>%
mutate(
lnCVR = map_dbl(model_lnCVR, pluck(2)), lnCVR_lower = map_dbl(model_lnCVR, pluck(6)),
lnCVR_upper = map_dbl(model_lnCVR, pluck(7)), lnCVR_se = map_dbl(model_lnCVR, pluck(3))
))[, c(1, 4:7)]
add.row.hearing <- as.data.frame(t(c("Hearing", NA, NA, NA, NA))) %>% setNames(names(plot3.female.meta.CVR.b))
plot3.female.meta.CVR.b <- bind_rows(plot3.female.meta.CVR.b, add.row.hearing)
plot3.female.meta.CVR.b <- plot3.female.meta.CVR.b[order(plot3.female.meta.CVR.b$GroupingTerm), ]
plot3.female.meta.VR.b <- as.data.frame(plot3.female.meta.VR %>% group_by(GroupingTerm) %>%
mutate(
lnVR = map_dbl(model_lnVR, pluck(2)), lnVR_lower = map_dbl(model_lnVR, pluck(6)),
lnVR_upper = map_dbl(model_lnVR, pluck(7)), lnVR_se = map_dbl(model_lnVR, pluck(3))
))[, c(1, 4:7)]
plot3.female.meta.VR.b <- plot3.female.meta.VR.b[order(plot3.female.meta.VR.b$GroupingTerm), ]
plot3.female.meta.RR.b <- as.data.frame(plot3.female.meta.RR %>% group_by(GroupingTerm) %>%
mutate(
lnRR = map_dbl(model_lnRR, pluck(2)), lnRR_lower = map_dbl(model_lnRR, pluck(6)),
lnRR_upper = map_dbl(model_lnRR, pluck(7)), lnRR_se = map_dbl(model_lnRR, pluck(3))
))[, c(1, 4:7)]
plot3.female.meta.RR.b <- plot3.female.meta.RR.b[order(plot3.female.meta.RR.b$GroupingTerm), ]
overall.female.plot3 <- full_join(plot3.female.meta.CVR.b, plot3.female.meta.VR.b)
overall.female.plot3 <- full_join(overall.female.plot3, plot3.female.meta.RR.b)
overall.female.plot3$GroupingTerm <- factor(overall.female.plot3$GroupingTerm, levels = c("Behaviour", "Morphology", "Metabolism", "Physiology", "Immunology", "Hematology", "Heart", "Hearing", "Eye", "All"))
overall.female.plot3$GroupingTerm <- factor(overall.female.plot3$GroupingTerm, rev(levels(overall.female.plot3$GroupingTerm)))Restructure data for plotting
overall3.female.sig <- gather(overall.female.plot3, parameter, value, c(lnCVR, lnRR), factor_key = TRUE) # lnVR,
lnCVR.ci <- overall3.female.sig %>%
filter(parameter == "lnCVR") %>%
mutate(ci.low = lnCVR_lower, ci.high = lnCVR_upper)
# lnVR.ci <- overall3.female.sig %>% filter(parameter == "lnVR") %>% mutate(ci.low = lnVR_lower, ci.high = lnVR_upper)
lnRR.ci <- overall3.female.sig %>%
filter(parameter == "lnRR") %>%
mutate(ci.low = lnRR_lower, ci.high = lnRR_upper)
overall4.female.sig <- bind_rows(lnCVR.ci, lnRR.ci) %>% select(GroupingTerm, parameter, value, ci.low, ci.high) # lnVR.ci,
overall4.female.sig$label <- "CI not overlapping zero"Plot Fig5B all significant results (CI not overlapping zero, female )
Metameta_Fig3_female.sig <- overall4.female.sig %>%
ggplot(aes(y = GroupingTerm, x = value)) +
geom_errorbarh(aes(
xmin = ci.low,
xmax = ci.high
),
height = 0.1, show.legend = FALSE
) +
geom_point(aes(shape = parameter),
fill = "salmon1", color = "salmon1", size = 2.2,
show.legend = FALSE
) +
scale_x_continuous(
limits = c(-0.4, 0),
breaks = c(-0.3, 0),
name = "Effect size"
) +
geom_vline(
xintercept = 0,
color = "black",
linetype = "dashed"
) +
facet_grid(
cols = vars(parameter), # rows = vars(label),
# labeller = label_wrap_gen(width = 23),
scales = "free",
space = "free"
) +
theme_bw() +
theme(
strip.text.y = element_text(angle = 270, size = 10, margin = margin(t = 15, r = 15, b = 15, l = 15)),
strip.text.x = element_text(size = 12),
strip.background = element_rect(colour = NULL, linetype = "blank", fill = "gray90"),
text = element_text(size = 14),
panel.spacing = unit(0.5, "lines"),
panel.border = element_blank(),
axis.line = element_line(),
panel.grid.major.x = element_line(linetype = "solid", colour = "gray95"),
panel.grid.major.y = element_line(linetype = "solid", color = "gray95"),
panel.grid.minor.y = element_blank(),
panel.grid.minor.x = element_blank(),
legend.title = element_blank(),
axis.title.x = element_blank(),
axis.title.y = element_blank()
)
# Metameta_Fig3_female.sig (Figure 5B left panel)Prepare data for traits with m/f difference > 10%
create column with 1= larger, 0= diff not larger than 10%
meta.male.plot3.perc <- metacombo %>%
mutate(
percCVR = ifelse(lnCVR > log(11 / 10), 1, 0),
percVR = ifelse(lnVR > log(11 / 10), 1, 0),
percRR = ifelse(lnRR > log(11 / 10), 1, 0)
)
# Significant subset for lnCVR
metacombo_male.plot3.CVR.perc <- meta.male.plot3.perc %>%
filter(percCVR == 1) %>%
group_by(GroupingTerm) %>%
nest()
metacombo_male.plot3.CVR.perc.all <- meta.male.plot3.perc %>%
filter(percCVR == 1) %>%
nest()
# Significant subset for lnVR
metacombo_male.plot3.VR.perc <- meta.male.plot3.perc %>%
filter(percVR == 1) %>%
group_by(GroupingTerm) %>%
nest()
metacombo_male.plot3.VR.perc.all <- meta.male.plot3.perc %>%
filter(percVR == 1) %>%
nest()
# Significant subset for lnRR
metacombo_male.plot3.RR.perc <- meta.male.plot3.perc %>%
filter(percRR == 1) %>%
group_by(GroupingTerm) %>%
nest()
metacombo_male.plot3.RR.perc.all <- meta.male.plot3.perc %>%
filter(percRR == 1) %>%
nest()
# **Final fixed effects meta-analyses within grouping terms and across grouping terms, with SE of the estimate
plot3.male.meta.CVR.perc <- metacombo_male.plot3.CVR.perc %>%
mutate(model_lnCVR = map(data, ~ metafor::rma.uni(
yi = .x$lnCVR, sei = (.x$lnCVR_upper - .x$lnCVR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
)))
plot3.male.meta.VR.perc <- metacombo_male.plot3.VR.perc %>%
mutate(model_lnVR = map(data, ~ metafor::rma.uni(
yi = .x$lnVR, sei = (.x$lnVR_upper - .x$lnVR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
)))
plot3.male.meta.RR.perc <- metacombo_male.plot3.RR.perc %>%
mutate(model_lnRR = map(data, ~ metafor::rma.uni(
yi = .x$lnRR, sei = (.x$lnRR_upper - .x$lnRR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
)))
# Across all grouping terms #
plot3.male.meta.CVR.perc.all <- metacombo_male.plot3.CVR.perc.all %>%
mutate(model_lnCVR = map(data, ~ metafor::rma.uni(
yi = .x$lnCVR, sei = (.x$lnCVR_upper - .x$lnCVR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
)))
plot3.male.meta.CVR.perc.all <- plot3.male.meta.CVR.perc.all %>% mutate(GroupingTerm = "All")
plot3.male.meta.VR.perc.all <- metacombo_male.plot3.VR.perc.all %>%
mutate(model_lnVR = map(data, ~ metafor::rma.uni(
yi = .x$lnVR, sei = (.x$lnVR_upper - .x$lnVR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
)))
plot3.male.meta.VR.perc.all <- plot3.male.meta.VR.perc.all %>% mutate(GroupingTerm = "All")
plot3.male.meta.RR.perc.all <- metacombo_male.plot3.RR.perc.all %>%
mutate(model_lnRR = map(data, ~ metafor::rma.uni(
yi = .x$lnRR, sei = (.x$lnRR_upper - .x$lnRR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
)))
plot3.male.meta.RR.perc.all <- plot3.male.meta.RR.perc.all %>% mutate(GroupingTerm = "All")
# Combine with separate grouping term results
plot3.male.meta.CVR.perc <- bind_rows(plot3.male.meta.CVR.perc, plot3.male.meta.CVR.perc.all)
plot3.male.meta.VR.perc <- bind_rows(plot3.male.meta.VR.perc, plot3.male.meta.VR.perc.all)
plot3.male.meta.RR.perc <- bind_rows(plot3.male.meta.RR.perc, plot3.male.meta.RR.perc.all)
# **Re-structure data for each grouping term; delete un-used variables: "Hearing missing for all 3 parameters"
plot3.male.meta.CVR.perc.b <- as.data.frame(plot3.male.meta.CVR.perc %>% group_by(GroupingTerm) %>%
mutate(
lnCVR = map_dbl(model_lnCVR, pluck(2)), lnCVR_lower = map_dbl(model_lnCVR, pluck(6)),
lnCVR_upper = map_dbl(model_lnCVR, pluck(7)), lnCVR_se = map_dbl(model_lnCVR, pluck(3))
))[, c(1, 4:7)]
add.row.hearing <- as.data.frame(t(c("Hearing", NA, NA, NA, NA))) %>% setNames(names(plot3.male.meta.CVR.perc.b))
plot3.male.meta.CVR.perc.b <- rbind(plot3.male.meta.CVR.perc.b, add.row.hearing)
plot3.male.meta.CVR.perc.b <- plot3.male.meta.CVR.perc.b[order(plot3.male.meta.CVR.perc.b$GroupingTerm), ]
plot3.male.meta.VR.perc.b <- as.data.frame(plot3.male.meta.VR.perc %>% group_by(GroupingTerm) %>%
mutate(
lnVR = map_dbl(model_lnVR, pluck(2)), lnVR_lower = map_dbl(model_lnVR, pluck(6)),
lnVR_upper = map_dbl(model_lnVR, pluck(7)), lnVR_se = map_dbl(model_lnVR, pluck(3))
))[, c(1, 4:7)]
add.row.hearing <- as.data.frame(t(c("Hearing", NA, NA, NA, NA))) %>% setNames(names(plot3.male.meta.VR.perc.b))
plot3.male.meta.VR.perc.b <- rbind(plot3.male.meta.VR.perc.b, add.row.hearing)
plot3.male.meta.VR.perc.b <- plot3.male.meta.VR.perc.b[order(plot3.male.meta.VR.perc.b$GroupingTerm), ]
plot3.male.meta.RR.perc.b <- as.data.frame(plot3.male.meta.RR.perc %>% group_by(GroupingTerm) %>%
mutate(
lnRR = map_dbl(model_lnRR, pluck(2)), lnRR_lower = map_dbl(model_lnRR, pluck(6)),
lnRR_upper = map_dbl(model_lnRR, pluck(7)), lnRR_se = map_dbl(model_lnRR, pluck(3))
))[, c(1, 4:7)]
add.row.hearing <- as.data.frame(t(c("Hearing", NA, NA, NA, NA))) %>%
setNames(names(plot3.male.meta.RR.perc.b))
plot3.male.meta.RR.perc.b <- rbind(plot3.male.meta.RR.perc.b, add.row.hearing)
add.row.eye <- as.data.frame(t(c("Eye", NA, NA, NA, NA))) %>%
setNames(names(plot3.male.meta.RR.perc.b))
plot3.male.meta.RR.perc.b <- rbind(plot3.male.meta.RR.perc.b, add.row.eye)
plot3.male.meta.RR.perc.b <- plot3.male.meta.RR.perc.b[order(plot3.male.meta.RR.perc.b$GroupingTerm), ]
plot3.male.meta.CVR.Vr.perc <- full_join(plot3.male.meta.CVR.perc.b, plot3.male.meta.VR.perc.b)
overall.male.plot3.perc <- full_join(plot3.male.meta.CVR.Vr.perc, plot3.male.meta.RR.perc.b)
overall.male.plot3.perc$GroupingTerm <- factor(overall.male.plot3.perc$GroupingTerm, levels = c("Behaviour", "Morphology", "Metabolism", "Physiology", "Immunology", "Hematology", "Heart", "Hearing", "Eye", "All"))
overall.male.plot3.perc$GroupingTerm <- factor(overall.male.plot3.perc$GroupingTerm, rev(levels(overall.male.plot3.perc$GroupingTerm)))Restructure data for plotting : Male biased, 10% difference
overall3.perc <- gather(overall.male.plot3.perc, parameter, value, c(lnCVR, lnRR), factor_key = TRUE) # lnVR,
lnCVR.ci <- overall3.perc %>%
filter(parameter == "lnCVR") %>%
mutate(ci.low = lnCVR_lower, ci.high = lnCVR_upper)
# lnVR.ci <- overall3.perc %>% filter(parameter == "lnVR") %>% mutate(ci.low = lnVR_lower, ci.high = lnVR_upper)
lnRR.ci <- overall3.perc %>%
filter(parameter == "lnRR") %>%
mutate(ci.low = lnRR_lower, ci.high = lnRR_upper)
overall4.male.perc <- bind_rows(lnCVR.ci, lnRR.ci) %>% select(GroupingTerm, parameter, value, ci.low, ci.high) # lnVR.ci,
overall4.male.perc$label <- "Sex difference in m/f ratios > 10%"
overall4.male.perc$value <- as.numeric(overall4.male.perc$value)
overall4.male.perc$ci.low <- as.numeric(overall4.male.perc$ci.low)
overall4.male.perc$ci.high <- as.numeric(overall4.male.perc$ci.high)Plot Fig5D all >10% difference (male bias)
Metameta_Fig3_male.perc <- overall4.male.perc %>% # filter(., GroupingTerm != "Hearing") %>%
ggplot(aes(y = GroupingTerm, x = value)) +
geom_errorbarh(aes(
xmin = ci.low,
xmax = ci.high
),
height = 0.1, show.legend = FALSE
) +
geom_point(aes(
shape = parameter,
fill = parameter
),
color = "mediumaquamarine", size = 2.2,
show.legend = FALSE
) +
scale_x_continuous(
limits = c(-0.2, 0.62),
breaks = c(0, 0.3),
name = "Effect size"
) +
geom_vline(
xintercept = 0,
color = "black",
linetype = "dashed"
) +
facet_grid(
cols = vars(parameter), rows = vars(label),
labeller = label_wrap_gen(width = 23),
scales = "free",
space = "free"
) +
theme_bw() +
theme(
strip.text.y = element_text(angle = 270, size = 10, margin = margin(t = 15, r = 15, b = 15, l = 15)),
strip.text.x = element_blank(),
strip.background = element_rect(colour = NULL, linetype = "blank", fill = "gray90"),
text = element_text(size = 14),
panel.spacing = unit(0.5, "lines"),
panel.border = element_blank(),
axis.line = element_line(),
panel.grid.major.x = element_line(linetype = "solid", colour = "gray95"),
panel.grid.major.y = element_line(linetype = "solid", color = "gray95"),
panel.grid.minor.y = element_blank(),
panel.grid.minor.x = element_blank(),
legend.title = element_blank(),
axis.title.x = element_text(hjust = 0.5, size = 14),
axis.title.y = element_blank()
)
# Metameta_Fig3_male.perc (Figure 5D right panel)
meta.plot3.perc <- metacombo %>%
mutate(
percCVR = ifelse(lnCVR < log(9 / 10), 1, 0),
percVR = ifelse(lnVR < log(9 / 10), 1, 0),
percRR = ifelse(lnRR < log(9 / 10), 1, 0)
)
# Significant subset for lnCVR
metacombo_plot3.CVR.perc <- meta.plot3.perc %>%
filter(percCVR == 1) %>%
group_by(GroupingTerm) %>%
nest()
metacombo_plot3.CVR.perc.all <- meta.plot3.perc %>%
filter(percCVR == 1) %>%
nest()
# Significant subset for lnVR
metacombo_plot3.VR.perc <- meta.plot3.perc %>%
filter(percVR == 1) %>%
group_by(GroupingTerm) %>%
nest()
metacombo_plot3.VR.perc.all <- meta.plot3.perc %>%
filter(percVR == 1) %>%
nest()
# Significant subset for lnRR
metacombo_plot3.RR.perc <- meta.plot3.perc %>%
filter(percRR == 1) %>%
group_by(GroupingTerm) %>%
nest()
metacombo_plot3.RR.perc.all <- meta.plot3.perc %>%
filter(percRR == 1) %>%
nest()
# **Final fixed effects meta-analyses within grouping terms, with SE of the estimate
plot3.meta.CVR.perc <- metacombo_plot3.CVR.perc %>%
mutate(model_lnCVR = map(data, ~ metafor::rma.uni(
yi = .x$lnCVR, sei = (.x$lnCVR_upper - .x$lnCVR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
)))
plot3.meta.VR.perc <- metacombo_plot3.VR.perc %>%
mutate(model_lnVR = map(data, ~ metafor::rma.uni(
yi = .x$lnVR, sei = (.x$lnVR_upper - .x$lnVR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
)))
plot3.meta.RR.perc <- metacombo_plot3.RR.perc %>%
mutate(model_lnRR = map(data, ~ metafor::rma.uni(
yi = .x$lnRR, sei = (.x$lnRR_upper - .x$lnRR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
)))
# Across all grouping terms #
plot3.meta.CVR.perc.all <- metacombo_plot3.CVR.perc.all %>%
mutate(model_lnCVR = map(data, ~ metafor::rma.uni(
yi = .x$lnCVR, sei = (.x$lnCVR_upper - .x$lnCVR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
)))
plot3.meta.CVR.perc.all <- plot3.meta.CVR.perc.all %>% mutate(GroupingTerm = "All")
plot3.meta.VR.perc.all <- metacombo_plot3.VR.perc.all %>%
mutate(model_lnVR = map(data, ~ metafor::rma.uni(
yi = .x$lnVR, sei = (.x$lnVR_upper - .x$lnVR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
)))
plot3.meta.VR.perc.all <- plot3.meta.VR.perc.all %>% mutate(GroupingTerm = "All")
plot3.meta.RR.perc.all <- metacombo_plot3.RR.perc.all %>%
mutate(model_lnRR = map(data, ~ metafor::rma.uni(
yi = .x$lnRR, sei = (.x$lnRR_upper - .x$lnRR_lower) / (2 * 1.96),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), verbose = F
)))
plot3.meta.RR.perc.all <- plot3.meta.RR.perc.all %>% mutate(GroupingTerm = "All")
# Combine with separate grouping term results
plot3.meta.CVR.perc <- bind_rows(plot3.meta.CVR.perc, plot3.meta.CVR.perc.all)
plot3.meta.VR.perc <- bind_rows(plot3.meta.VR.perc, plot3.meta.VR.perc.all)
plot3.meta.RR.perc <- bind_rows(plot3.meta.RR.perc, plot3.meta.RR.perc.all)
# **Re-structure data for each grouping term; delete un-used variables: "Hearing missing for all 3 parameters"
plot3.meta.CVR.perc.b <- as.data.frame(plot3.meta.CVR.perc %>% group_by(GroupingTerm) %>%
mutate(
lnCVR = map_dbl(model_lnCVR, pluck(2)), lnCVR_lower = map_dbl(model_lnCVR, pluck(6)),
lnCVR_upper = map_dbl(model_lnCVR, pluck(7)), lnCVR_se = map_dbl(model_lnCVR, pluck(3))
))[, c(1, 4:7)]
add.row.hearing <- as.data.frame(t(c("Hearing", NA, NA, NA, NA))) %>% setNames(names(plot3.meta.CVR.perc.b))
plot3.meta.CVR.perc.b <- rbind(plot3.meta.CVR.perc.b, add.row.hearing)
plot3.meta.CVR.perc.b <- plot3.meta.CVR.perc.b[order(plot3.meta.CVR.perc.b$GroupingTerm), ]
plot3.meta.VR.perc.b <- as.data.frame(plot3.meta.VR.perc %>% group_by(GroupingTerm) %>%
mutate(
lnVR = map_dbl(model_lnVR, pluck(2)), lnVR_lower = map_dbl(model_lnVR, pluck(6)),
lnVR_upper = map_dbl(model_lnVR, pluck(7)), lnVR_se = map_dbl(model_lnVR, pluck(3))
))[, c(1, 4:7)]
add.row.hearing <- as.data.frame(t(c("Hearing", NA, NA, NA, NA))) %>% setNames(names(plot3.meta.VR.perc.b))
plot3.meta.VR.perc.b <- rbind(plot3.meta.VR.perc.b, add.row.hearing)
plot3.meta.VR.perc.b <- plot3.meta.VR.perc.b[order(plot3.meta.VR.perc.b$GroupingTerm), ]
plot3.meta.RR.perc.b <- as.data.frame(plot3.meta.RR.perc %>% group_by(GroupingTerm) %>%
mutate(
lnRR = map_dbl(model_lnRR, pluck(2)), lnRR_lower = map_dbl(model_lnRR, pluck(6)),
lnRR_upper = map_dbl(model_lnRR, pluck(7)), lnRR_se = map_dbl(model_lnRR, pluck(3))
))[, c(1, 4:7)]
add.row.hearing <- as.data.frame(t(c("Hearing", NA, NA, NA, NA))) %>% setNames(names(plot3.meta.RR.perc.b))
plot3.meta.RR.perc.b <- rbind(plot3.meta.RR.perc.b, add.row.hearing)
add.row.hematology <- as.data.frame(t(c("Hematology", NA, NA, NA, NA))) %>%
setNames(names(plot3.meta.RR.perc.b))
plot3.meta.RR.perc.b <- rbind(plot3.meta.RR.perc.b, add.row.hematology)
plot3.meta.RR.perc.b <- plot3.meta.RR.perc.b[order(plot3.meta.RR.perc.b$GroupingTerm), ]
plot3.meta.CVR.perc.c <- full_join(plot3.meta.CVR.perc.b, plot3.meta.VR.perc.b)
overall.plot3.perc <- full_join(plot3.meta.CVR.perc.c, plot3.meta.RR.perc.b)
overall.plot3.perc$GroupingTerm <- factor(overall.plot3.perc$GroupingTerm, levels = c("Behaviour", "Morphology", "Metabolism", "Physiology", "Immunology", "Hematology", "Heart", "Hearing", "Eye", "All"))
overall.plot3.perc$GroupingTerm <- factor(overall.plot3.perc$GroupingTerm, rev(levels(overall.plot3.perc$GroupingTerm)))Restructure data for plotting Female bias, 10 percent difference
overall3.perc <- gather(overall.plot3.perc, parameter, value, c(lnCVR, lnRR), factor_key = TRUE) # lnVR,
lnCVR.ci <- overall3.perc %>%
filter(parameter == "lnCVR") %>%
mutate(ci.low = lnCVR_lower, ci.high = lnCVR_upper)
# lnVR.ci <- overall3.perc %>% filter(parameter == "lnVR") %>% mutate(ci.low = lnVR_lower, ci.high = lnVR_upper)
lnRR.ci <- overall3.perc %>%
filter(parameter == "lnRR") %>%
mutate(ci.low = lnRR_lower, ci.high = lnRR_upper)
overall4.perc <- bind_rows(lnCVR.ci, lnRR.ci) %>% select(GroupingTerm, parameter, value, ci.low, ci.high) # lnVR.ci,
overall4.perc$label <- "Sex difference in m/f ratios > 10%"
overall4.perc$value <- as.numeric(overall4.perc$value)
overall4.perc$ci.low <- as.numeric(overall4.perc$ci.low)
overall4.perc$ci.high <- as.numeric(overall4.perc$ci.high)Plot Fig5D all >10% difference (female)
Metameta_Fig3_female.perc <- overall4.perc %>%
ggplot(aes(y = GroupingTerm, x = value)) +
geom_errorbarh(aes(
xmin = ci.low,
xmax = ci.high
),
height = 0.1, show.legend = FALSE
) +
geom_point(aes(shape = parameter),
fill = "salmon1", color = "salmon1", size = 2.2,
show.legend = FALSE
) +
# scale_shape_manual(values =
scale_x_continuous(
limits = c(-0.53, 0.2),
breaks = c(-0.3, 0),
name = "Effect size"
) +
geom_vline(
xintercept = 0,
color = "black",
linetype = "dashed"
) +
facet_grid(
cols = vars(parameter), # rows = vars(label),
# labeller = label_wrap_gen(width = 23),
scales = "free",
space = "free"
) +
theme_bw() +
theme(
strip.text.y = element_text(angle = 270, size = 10, margin = margin(t = 15, r = 15, b = 15, l = 15)),
strip.text.x = element_blank(),
strip.background = element_rect(colour = NULL, linetype = "blank", fill = "gray90"),
text = element_text(size = 14),
panel.spacing = unit(0.5, "lines"),
panel.border = element_blank(),
axis.line = element_line(),
panel.grid.major.x = element_line(linetype = "solid", colour = "gray95"),
panel.grid.major.y = element_line(linetype = "solid", color = "gray95"),
panel.grid.minor.y = element_blank(),
panel.grid.minor.x = element_blank(),
legend.title = element_blank(),
axis.title.x = element_text(hjust = 0.5, size = 14),
axis.title.y = element_blank()
)
# Metameta_Fig3_female.perc (Figure 5D left panel)library(ggpubr)
Fig5b <- ggarrange(Metameta_Fig3_female.sig, Metameta_Fig3_male.sig,
ncol = 2, nrow = 1, widths = c(1, 1.20), heights = c(1, 1)
)
Fig5d <- ggarrange(Metameta_Fig3_female.perc, Metameta_Fig3_male.perc,
ncol = 2, nrow = 1, widths = c(1, 1.20), heights = c(1, 1)
)
# end combination Figure 5
Fig5 <- ggarrange(malebias_Fig2_sigtraits, malebias_Fig2_over10, Fig5b, Fig5d, ncol = 1, nrow = 4, heights = c(2.3, 2, 2.1, 2), labels = c("A", " ", "B", " "))
Fig5Create matrix to store results for all traits
results.allhetero.grouping <- as.data.frame(cbind(c(1:n), matrix(rep(0, n * 30), ncol = 30)))
names(results.allhetero.grouping) <- c(
"id", "sigma2_strain.CVR", "sigma2_center.CVR", "sigma2_error.CVR", "s.nlevels.strain.CVR",
"s.nlevels.center.CVR", "s.nlevels.error.CVR", "sigma2_strain.VR", "sigma2_center.VR", "sigma2_error.VR", "s.nlevels.strain.VR",
"s.nlevels.center.VR", "s.nlevels.error.VR", "sigma2_strain.RR", "sigma2_center.RR", "sigma2_error.RR", "s.nlevels.strain.RR",
"s.nlevels.center.RR", "s.nlevels.error.RR", "lnCVR", "lnCVR_lower", "lnCVR_upper", "lnCVR_se", "lnVR", "lnVR_lower", "lnVR_upper",
"lnVR_se", "lnRR", "lnRR_lower", "lnRR_upper", "lnRR_se"
)LOOP Parameters to extract from metafor (sigma2’s, s.nlevels)
for (t in 1:n) {
tryCatch(
{
data_par_age <- data_subset_parameterid_individual_by_age(data, t, age_min = 0, age_center = 100)
population_stats <- calculate_population_stats(data_par_age)
results <- create_meta_analysis_effect_sizes(population_stats)
# lnCVR, logaritm of the ratio of male and female coefficients of variance
cvr. <- metafor::rma.mv(yi = effect_size_CVR, V = sample_variance_CVR, random = list(
~ 1 | strain_name, ~ 1 | production_center,
~ 1 | err
), control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), data = results)
results.allhetero.grouping[t, 2] <- cvr.$sigma2[1]
results.allhetero.grouping[t, 3] <- cvr.$sigma2[2]
results.allhetero.grouping[t, 4] <- cvr.$sigma2[3]
results.allhetero.grouping[t, 5] <- cvr.$s.nlevels[1]
results.allhetero.grouping[t, 6] <- cvr.$s.nlevels[2]
results.allhetero.grouping[t, 7] <- cvr.$s.nlevels[3]
results.allhetero.grouping[t, 20] <- cvr.$b
results.allhetero.grouping[t, 21] <- cvr.$ci.lb
results.allhetero.grouping[t, 22] <- cvr.$ci.ub
results.allhetero.grouping[t, 23] <- cvr.$se
# lnVR, male to female variability ratio (logarithm of male and female standard deviations)
vr. <- metafor::rma.mv(yi = effect_size_VR, V = sample_variance_VR, random = list(
~ 1 | strain_name, ~ 1 | production_center,
~ 1 | err
), control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), data = results)
results.allhetero.grouping[t, 8] <- vr.$sigma2[1]
results.allhetero.grouping[t, 9] <- vr.$sigma2[2]
results.allhetero.grouping[t, 10] <- vr.$sigma2[3]
results.allhetero.grouping[t, 11] <- vr.$s.nlevels[1]
results.allhetero.grouping[t, 12] <- vr.$s.nlevels[2]
results.allhetero.grouping[t, 13] <- vr.$s.nlevels[3]
results.allhetero.grouping[t, 24] <- vr.$b
results.allhetero.grouping[t, 25] <- vr.$ci.lb
results.allhetero.grouping[t, 26] <- vr.$ci.ub
results.allhetero.grouping[t, 27] <- vr.$se
# lnRR, response ratio (logarithm of male and female means)
rr. <- metafor::rma.mv(yi = effect_size_RR, V = sample_variance_RR, random = list(
~ 1 | strain_name, ~ 1 | production_center,
~ 1 | err
), control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 1000), data = results)
results.allhetero.grouping[t, 14] <- rr.$sigma2[1]
results.allhetero.grouping[t, 15] <- rr.$sigma2[2]
results.allhetero.grouping[t, 16] <- rr.$sigma2[3]
results.allhetero.grouping[t, 17] <- rr.$s.nlevels[1]
results.allhetero.grouping[t, 18] <- rr.$s.nlevels[2]
results.allhetero.grouping[t, 19] <- rr.$s.nlevels[3]
results.allhetero.grouping[t, 28] <- rr.$b
results.allhetero.grouping[t, 29] <- rr.$ci.lb
results.allhetero.grouping[t, 30] <- rr.$ci.ub
results.allhetero.grouping[t, 31] <- rr.$se
},
error = function(e) {
cat("ERROR :", conditionMessage(e), "\n")
}
)
}results.allhetero.grouping2 <- results.allhetero.grouping[results.allhetero.grouping$s.nlevels.strain.VR != 0, ]
# nrow(results.allhetero.grouping2) #218Merge data sets containing metafor results with procedure etc. names
# procedures <- read.csv(here("export", "procedures.csv"))
results.allhetero.grouping2$parameter_group <- data$parameter_group[match(results.allhetero.grouping2$id, data$id)]
results.allhetero.grouping2$procedure <- data$procedure_name[match(results.allhetero.grouping2$id, data$id)]
results.allhetero.grouping2$GroupingTerm <- procedures$GroupingTerm[match(results.allhetero.grouping2$procedure, procedures$procedure)]
results.allhetero.grouping2$parameter_name <- data$parameter_name[match(results.allhetero.grouping2$id, data$id)]## *Perform meta-meta-analysis (3 for each of the 9 grouping terms: var.CVR, var.VR, var.RR)
metacombohetero_final <- metacombohetero %>%
group_by(GroupingTerm) %>%
nest()
# Final fixed effects meta-analyses within grouping terms, with SE of the estimate
# metacombohetero$var.CVR
heterog1 <- metacombohetero_final %>%
mutate(
model_heteroCVR = map(data, ~ metafor::rma.uni(
yi = .x$var.CVR, sei = sqrt(1 / 2 * (.x$N.CVR - 1)),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 10000, stepadj = 0.5), verbose = F
)),
model_heteroVR = map(data, ~ metafor::rma.uni(
yi = .x$var.VR, sei = sqrt(1 / 2 * (.x$N.VR - 1)),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 10000, stepadj = 0.5), verbose = F
)),
model_heteroRR = map(data, ~ metafor::rma.uni(
yi = .x$var.RR, sei = sqrt(1 / 2 * (.x$N.RR - 1)),
control = list(optimizer = "optim", optmethod = "Nelder-Mead", maxit = 10000, stepadj = 0.5), verbose = F
))
)
# **Re-structure data for each grouping term; extract heterogenenity/variance terms; delete un-used variables
Behaviour. <- heterog1 %>%
filter(., GroupingTerm == "Behaviour") %>%
select(., -data) %>%
mutate(
heteroCVR = .[[2]][[1]]$b, heteroCVR_lower = .[[2]][[1]]$ci.lb, heteroCVR_upper = .[[2]][[1]]$ci.ub, heteroCVR_se = .[[2]][[1]]$se,
heteroVR = .[[3]][[1]]$b, heteroVR_lower = .[[3]][[1]]$ci.lb, heteroVR_upper = .[[3]][[1]]$ci.ub, heteroVR_se = .[[3]][[1]]$se,
heteroRR = .[[4]][[1]]$b, heteroRR_lower = .[[4]][[1]]$ci.lb, heteroRR_upper = .[[4]][[1]]$ci.ub, heteroRR_se = .[[4]][[1]]$se
) %>%
select(., GroupingTerm, heteroCVR:heteroRR_se)
Immunology. <- heterog1 %>%
filter(., GroupingTerm == "Immunology") %>%
select(., -data) %>%
mutate(
heteroCVR = .[[2]][[1]]$b, heteroCVR_lower = .[[2]][[1]]$ci.lb, heteroCVR_upper = .[[2]][[1]]$ci.ub, heteroCVR_se = .[[2]][[1]]$se,
heteroVR = .[[3]][[1]]$b, heteroVR_lower = .[[3]][[1]]$ci.lb, heteroVR_upper = .[[3]][[1]]$ci.ub, heteroVR_se = .[[3]][[1]]$se,
heteroRR = .[[4]][[1]]$b, heteroRR_lower = .[[4]][[1]]$ci.lb, heteroRR_upper = .[[4]][[1]]$ci.ub, heteroRR_se = .[[4]][[1]]$se
) %>%
select(., GroupingTerm, heteroCVR:heteroRR_se)
Hematology. <- heterog1 %>%
filter(., GroupingTerm == "Hematology") %>%
select(., -data) %>%
mutate(
heteroCVR = .[[2]][[1]]$b, heteroCVR_lower = .[[2]][[1]]$ci.lb, heteroCVR_upper = .[[2]][[1]]$ci.ub, heteroCVR_se = .[[2]][[1]]$se,
heteroVR = .[[3]][[1]]$b, heteroVR_lower = .[[3]][[1]]$ci.lb, heteroVR_upper = .[[3]][[1]]$ci.ub, heteroVR_se = .[[3]][[1]]$se,
heteroRR = .[[4]][[1]]$b, heteroRR_lower = .[[4]][[1]]$ci.lb, heteroRR_upper = .[[4]][[1]]$ci.ub, heteroRR_se = .[[4]][[1]]$se
) %>%
select(., GroupingTerm, heteroCVR:heteroRR_se)
Hearing. <- heterog1 %>%
filter(., GroupingTerm == "Hearing") %>%
select(., -data) %>%
mutate(
heteroCVR = .[[2]][[1]]$b, heteroCVR_lower = .[[2]][[1]]$ci.lb, heteroCVR_upper = .[[2]][[1]]$ci.ub, heteroCVR_se = .[[2]][[1]]$se,
heteroVR = .[[3]][[1]]$b, heteroVR_lower = .[[3]][[1]]$ci.lb, heteroVR_upper = .[[3]][[1]]$ci.ub, heteroVR_se = .[[3]][[1]]$se,
heteroRR = .[[4]][[1]]$b, heteroRR_lower = .[[4]][[1]]$ci.lb, heteroRR_upper = .[[4]][[1]]$ci.ub, heteroRR_se = .[[4]][[1]]$se
) %>%
select(., GroupingTerm, heteroCVR:heteroRR_se)
Physiology. <- heterog1 %>%
filter(., GroupingTerm == "Physiology") %>%
select(., -data) %>%
mutate(
heteroCVR = .[[2]][[1]]$b, heteroCVR_lower = .[[2]][[1]]$ci.lb, heteroCVR_upper = .[[2]][[1]]$ci.ub, heteroCVR_se = .[[2]][[1]]$se,
heteroVR = .[[3]][[1]]$b, heteroVR_lower = .[[3]][[1]]$ci.lb, heteroVR_upper = .[[3]][[1]]$ci.ub, heteroVR_se = .[[3]][[1]]$se,
heteroRR = .[[4]][[1]]$b, heteroRR_lower = .[[4]][[1]]$ci.lb, heteroRR_upper = .[[4]][[1]]$ci.ub, heteroRR_se = .[[4]][[1]]$se
) %>%
select(., GroupingTerm, heteroCVR:heteroRR_se)
Metabolism. <- heterog1 %>%
filter(., GroupingTerm == "Metabolism") %>%
select(., -data) %>%
mutate(
heteroCVR = .[[2]][[1]]$b, heteroCVR_lower = .[[2]][[1]]$ci.lb, heteroCVR_upper = .[[2]][[1]]$ci.ub, heteroCVR_se = .[[2]][[1]]$se,
heteroVR = .[[3]][[1]]$b, heteroVR_lower = .[[3]][[1]]$ci.lb, heteroVR_upper = .[[3]][[1]]$ci.ub, heteroVR_se = .[[3]][[1]]$se,
heteroRR = .[[4]][[1]]$b, heteroRR_lower = .[[4]][[1]]$ci.lb, heteroRR_upper = .[[4]][[1]]$ci.ub, heteroRR_se = .[[4]][[1]]$se
) %>%
select(., GroupingTerm, heteroCVR:heteroRR_se)
Morphology. <- heterog1 %>%
filter(., GroupingTerm == "Morphology") %>%
select(., -data) %>%
mutate(
heteroCVR = .[[2]][[1]]$b, heteroCVR_lower = .[[2]][[1]]$ci.lb, heteroCVR_upper = .[[2]][[1]]$ci.ub, heteroCVR_se = .[[2]][[1]]$se,
heteroVR = .[[3]][[1]]$b, heteroVR_lower = .[[3]][[1]]$ci.lb, heteroVR_upper = .[[3]][[1]]$ci.ub, heteroVR_se = .[[3]][[1]]$se,
heteroRR = .[[4]][[1]]$b, heteroRR_lower = .[[4]][[1]]$ci.lb, heteroRR_upper = .[[4]][[1]]$ci.ub, heteroRR_se = .[[4]][[1]]$se
) %>%
select(., GroupingTerm, heteroCVR:heteroRR_se)
Heart. <- heterog1 %>%
filter(., GroupingTerm == "Heart") %>%
select(., -data) %>%
mutate(
heteroCVR = .[[2]][[1]]$b, heteroCVR_lower = .[[2]][[1]]$ci.lb, heteroCVR_upper = .[[2]][[1]]$ci.ub, heteroCVR_se = .[[2]][[1]]$se,
heteroVR = .[[3]][[1]]$b, heteroVR_lower = .[[3]][[1]]$ci.lb, heteroVR_upper = .[[3]][[1]]$ci.ub, heteroVR_se = .[[3]][[1]]$se,
heteroRR = .[[4]][[1]]$b, heteroRR_lower = .[[4]][[1]]$ci.lb, heteroRR_upper = .[[4]][[1]]$ci.ub, heteroRR_se = .[[4]][[1]]$se
) %>%
select(., GroupingTerm, heteroCVR:heteroRR_se)
Eye. <- heterog1 %>%
filter(., GroupingTerm == "Eye") %>%
select(., -data) %>%
mutate(
heteroCVR = .[[2]][[1]]$b, heteroCVR_lower = .[[2]][[1]]$ci.lb, heteroCVR_upper = .[[2]][[1]]$ci.ub, heteroCVR_se = .[[2]][[1]]$se,
heteroVR = .[[3]][[1]]$b, heteroVR_lower = .[[3]][[1]]$ci.lb, heteroVR_upper = .[[3]][[1]]$ci.ub, heteroVR_se = .[[3]][[1]]$se,
heteroRR = .[[4]][[1]]$b, heteroRR_lower = .[[4]][[1]]$ci.lb, heteroRR_upper = .[[4]][[1]]$ci.ub, heteroRR_se = .[[4]][[1]]$se
) %>%
select(., GroupingTerm, heteroCVR:heteroRR_se)
heterog2 <- bind_rows(Behaviour., Morphology., Metabolism., Physiology., Immunology., Hematology., Heart., Hearing., Eye.)
# str(heterog2)Restructure data for plotting
heterog3 <- gather(heterog2, parameter, value, c(heteroCVR, heteroVR, heteroRR), factor_key = TRUE)
heteroCVR.ci <- heterog3 %>%
filter(parameter == "heteroCVR") %>%
mutate(ci.low = heteroCVR_lower, ci.high = heteroCVR_upper)
heteroVR.ci <- heterog3 %>%
filter(parameter == "heteroVR") %>%
mutate(ci.low = heteroVR_lower, ci.high = heteroVR_upper)
heteroRR.ci <- heterog3 %>%
filter(parameter == "heteroRR") %>%
mutate(ci.low = heteroRR_lower, ci.high = heteroRR_upper)
heterog4 <- bind_rows(heteroCVR.ci, heteroVR.ci, heteroRR.ci) %>% select(GroupingTerm, parameter, value, ci.low, ci.high)
# **Re-order grouping terms
heterog4$GroupingTerm <- factor(heterog4$GroupingTerm, levels = c("Behaviour", "Morphology", "Metabolism", "Physiology", "Immunology", "Hematology", "Heart", "Hearing", "Eye"))
heterog4$GroupingTerm <- factor(heterog4$GroupingTerm, rev(levels(heterog4$GroupingTerm)))
heterog4$label <- "All traits"
# write.csv(heterog4, "heterog4.csv")Plot Fig4 all traits
heterog5 <- heterog4
heterog5$mean <- as.numeric(exp(heterog5$value))
heterog5$ci.l <- as.numeric(exp(heterog5$ci.low))
heterog5$ci.h <- as.numeric(exp(heterog5$ci.high))
heterog6 <- heterog5
Hetero4c <-
heterog6 %>%
filter(
parameter == "heteroCVR" | parameter == "heteroRR"
) %>%
ggplot(aes(y = GroupingTerm, x = mean)) +
geom_errorbarh(aes(
xmin = ci.l,
xmax = ci.h
),
height = 0.1, show.legend = FALSE
) +
geom_point(aes(shape = parameter),
fill = "black",
color = "black", size = 2.2,
show.legend = FALSE
) +
scale_x_continuous(
limits = c(-0.1, 1.4),
# breaks = c(0, 0.1, 0.2),
name = "sigma^2"
) +
# geom_vline(xintercept=0,
# color='black',
# linetype='dashed')+
facet_grid(
cols = vars(parameter), rows = vars(label),
labeller = label_wrap_gen(width = 23),
scales = "free",
space = "free"
) +
theme_bw() +
theme(
strip.text.y = element_text(angle = 270, size = 10, margin = margin(t = 15, r = 15, b = 15, l = 15)),
strip.text.x = element_text(size = 12),
strip.background = element_rect(colour = NULL, linetype = "blank", fill = "gray90"),
text = element_text(size = 14),
panel.spacing = unit(0.5, "lines"),
panel.border = element_blank(),
axis.line = element_line(),
panel.grid.major.x = element_line(linetype = "solid", colour = "gray95"),
panel.grid.major.y = element_line(linetype = "solid", color = "gray95"),
panel.grid.minor.y = element_blank(),
panel.grid.minor.x = element_blank(),
legend.title = element_blank(),
axis.title.x = element_text(hjust = 0.5, size = 14),
axis.title.y = element_blank()
)
# Hetero4c
# ggsave("Fig4.pdf", plot = Metameta_Fig4_alltraits, width = 7, height = 6)
Fig4 <- ggarrange(malebias_Fig2_alltraits, Metameta_Fig3_alltraits, Hetero4c, nrow = 3, align = "v", heights = c(1, 1, 1), labels = c("A", "B", "C"))
Fig4
# ggsave("Fig4_OverallResults.pdf", plot = Fig4, width = 6, height = 5)## Heterogneity, S1 C
HeteroS1 <- heterog5 %>%
ggplot(aes(y = GroupingTerm, x = mean)) +
geom_errorbarh(aes(
xmin = ci.l,
xmax = ci.h
),
height = 0.1, show.legend = FALSE
) +
geom_point(aes(shape = parameter),
fill = "black",
color = "black", size = 2.2,
show.legend = FALSE
) +
scale_x_continuous(
limits = c(-0.1, 1.4),
# breaks = c(0, 0.1, 0.2),
name = "Effect size"
) +
# geom_vline(xintercept=0,
# color='black',
# linetype='dashed')+
facet_grid(
cols = vars(parameter), rows = vars(label),
labeller = label_wrap_gen(width = 23),
scales = "free",
space = "free"
) +
theme_bw() +
theme(
strip.text.y = element_text(angle = 270, size = 10, margin = margin(t = 15, r = 15, b = 15, l = 15)),
strip.text.x = element_text(size = 12),
strip.background = element_rect(colour = NULL, linetype = "blank", fill = "gray90"),
text = element_text(size = 14),
panel.spacing = unit(0.5, "lines"),
panel.border = element_blank(),
axis.line = element_line(),
panel.grid.major.x = element_line(linetype = "solid", colour = "gray95"),
panel.grid.major.y = element_line(linetype = "solid", color = "gray95"),
panel.grid.minor.y = element_blank(),
panel.grid.minor.x = element_blank(),
legend.title = element_blank(),
axis.title.x = element_blank(),
axis.title.y = element_blank()
)
# HeteroS1
# ggsave("Fig4.pdf", plot = Metameta_Fig4_alltraits, width = 7, height = 6)# *Prepare data for all traits
meta.plot2.all <- meta_clean %>%
select(lnCVR, lnVR, lnRR, GroupingTerm) %>%
arrange(GroupingTerm)
meta.plot2.all.bS1 <- gather(meta.plot2.all, trait, value, c(lnCVR, lnVR, lnRR))
meta.plot2.all.bS1$trait <- factor(meta.plot2.all.bS1$trait, levels = c("lnCVR", "lnVR", "lnRR"))
meta.plot2.all.cS1 <- meta.plot2.all.bS1 %>%
group_by_at(vars(trait, GroupingTerm)) %>%
summarise(
malebias = sum(value > 0), femalebias = sum(value <= 0), total = malebias + femalebias,
malepercent = malebias * 100 / total, femalepercent = femalebias * 100 / total
)
meta.plot2.all.cS1$label <- "All traits"
# restructure to create stacked bar plots
meta.plot2.all.dS1 <- as.data.frame(meta.plot2.all.cS1)
meta.plot2.all.eS1 <- gather(meta.plot2.all.dS1, key = sex, value = percent, malepercent:femalepercent, factor_key = TRUE)
# create new sample size variable
meta.plot2.all.eS1$samplesize <- with(meta.plot2.all.eS1, ifelse(sex == "malepercent", malebias, femalebias))
malebias_FigS1_alltraits <-
ggplot(meta.plot2.all.eS1) +
aes(x = GroupingTerm, y = percent, fill = sex) +
geom_col() +
geom_hline(yintercept = 50, linetype = "dashed", color = "gray40") +
geom_text(
data = subset(meta.plot2.all.eS1, samplesize != 0), aes(label = samplesize), position = position_stack(vjust = .5),
color = "white", size = 3.5
) +
facet_grid(
cols = vars(trait), rows = vars(label), labeller = label_wrap_gen(width = 18),
scales = "free", space = "free"
) +
scale_fill_brewer(palette = "Set2") +
theme_bw(base_size = 18) +
theme(
strip.text.y = element_text(angle = 270, size = 10, margin = margin(t = 15, r = 15, b = 15, l = 15)),
strip.text.x = element_text(size = 12),
strip.background = element_rect(colour = NULL, linetype = "blank", fill = "gray90"),
text = element_text(size = 14),
panel.spacing = unit(0.5, "lines"),
panel.border = element_blank(),
axis.line = element_line(),
panel.grid.major.x = element_line(linetype = "solid", colour = "gray95"),
panel.grid.major.y = element_line(linetype = "solid", color = "gray95"),
panel.grid.minor.y = element_blank(),
panel.grid.minor.x = element_blank(),
legend.position = "none",
axis.title.x = element_blank(),
axis.title.y = element_blank()
) +
coord_flip()
# malebias_FigS1_alltraits #(panel A in Figure S1)Restructure MALE data for plotting
overall3.male.sigS <- gather(overall.male.plot3, parameter, value, c(lnCVR, lnVR, lnRR), factor_key = TRUE)
lnCVR.ci <- overall3.male.sigS %>%
filter(parameter == "lnCVR") %>%
mutate(ci.low = lnCVR_lower, ci.high = lnCVR_upper)
lnVR.ci <- overall3.male.sigS %>%
filter(parameter == "lnVR") %>%
mutate(ci.low = lnVR_lower, ci.high = lnVR_upper)
lnRR.ci <- overall3.male.sigS %>%
filter(parameter == "lnRR") %>%
mutate(ci.low = lnRR_lower, ci.high = lnRR_upper)
overall4.male.sigS <- bind_rows(lnCVR.ci, lnVR.ci, lnRR.ci) %>% select(GroupingTerm, parameter, value, ci.low, ci.high)
overall4.male.sigS$label <- "CI not overlapping zero"Data are restructured, and grouping terms are being re-ordered
overall3S <- gather(overall2, parameter, value, c(lnCVR, lnVR, lnRR), factor_key = TRUE)
lnCVR.ci <- overall3S %>%
filter(parameter == "lnCVR") %>%
mutate(ci.low = lnCVR_lower, ci.high = lnCVR_upper)
lnVR.ci <- overall3S %>%
filter(parameter == "lnVR") %>%
mutate(ci.low = lnVR_lower, ci.high = lnVR_upper)
lnRR.ci <- overall3S %>%
filter(parameter == "lnRR") %>%
mutate(ci.low = lnRR_lower, ci.high = lnRR_upper)
overall4S <- bind_rows(lnCVR.ci, lnVR.ci, lnRR.ci) %>% select(GroupingTerm, parameter, value, ci.low, ci.high)
# re-order Grouping Terms
overall4S$GroupingTerm <- factor(overall4S$GroupingTerm, levels = c("Behaviour", "Morphology", "Metabolism", "Physiology", "Immunology", "Hematology", "Heart", "Hearing", "Eye", "All"))
overall4S$GroupingTerm <- factor(overall4S$GroupingTerm, rev(levels(overall4S$GroupingTerm)))
overall4S$label <- "All traits"Preparation: Sub-Plot for Figure S1: all traits (S1 B)
Metameta_FigS1_alltraits <- overall4S %>%
ggplot(aes(y = GroupingTerm, x = value)) +
geom_errorbarh(aes(
xmin = ci.low,
xmax = ci.high
),
height = 0.1, show.legend = FALSE
) +
geom_point(aes(shape = parameter),
fill = "black",
color = "black", size = 2.2,
show.legend = FALSE
) +
scale_x_continuous(
limits = c(-0.24, 0.25),
breaks = c(-0.2, -0.1, 0, 0.1, 0.2),
name = "Effect size"
) +
geom_vline(
xintercept = 0,
color = "black",
linetype = "dashed"
) +
facet_grid(
cols = vars(parameter), rows = vars(label),
labeller = label_wrap_gen(width = 23),
scales = "free",
space = "free"
) +
theme_bw() +
theme(
strip.text.y = element_text(angle = 270, size = 10, margin = margin(t = 15, r = 15, b = 15, l = 15)),
strip.text.x = element_text(size = 12),
strip.background = element_rect(colour = NULL, linetype = "blank", fill = "gray90"),
text = element_text(size = 14),
panel.spacing = unit(0.5, "lines"),
panel.border = element_blank(),
axis.line = element_line(),
panel.grid.major.x = element_line(linetype = "solid", colour = "gray95"),
panel.grid.major.y = element_line(linetype = "solid", color = "gray95"),
panel.grid.minor.y = element_blank(),
panel.grid.minor.x = element_blank(),
legend.title = element_blank(),
axis.title.x = element_text(hjust = 0.5, size = 14),
axis.title.y = element_blank()
)
# Metameta_FigS1_alltraitsFigS1 <- ggarrange(malebias_FigS1_alltraits + xlab("percentage sex bias"), Metameta_FigS1_alltraits, HeteroS1, nrow = 3, align = "v", heights = c(1, 1, 1), labels = c("A", "B", "C"))
FigS1
# ggsave("FigS1_OverallResults.pdf", plot = Fig4, width = 6, height = 5)Plot FigS2 all significant results (CI not overlapping zero) for males
meta.plot2.sig.bS <- meta.plot2.sig[, c("lnCVR", "lnVR", "lnRR", "lnCVRsig", "lnVRsig", "lnRRsig", "GroupingTerm")]
meta.plot2.sig.cS <- gather(meta.plot2.sig.bS, trait, value, lnCVR:lnRR)
meta.plot2.sig.cS$sig <- "placeholder"
meta.plot2.sig.cS$trait <- factor(meta.plot2.sig.cS$trait, levels = c("lnCVR", "lnVR", "lnRR"))
meta.plot2.sig.cS$sig <- ifelse(meta.plot2.sig.cS$trait == "lnCVR", meta.plot2.sig.cS$lnCVRsig,
ifelse(meta.plot2.sig.cS$trait == "lnVR", meta.plot2.sig.cS$lnVRsig, meta.plot2.sig.cS$lnRRsig)
)
# choosing sex biased ln-ratios significantly larger than 0
meta.plotS2.sig.malebias <- meta.plot2.sig.cS %>%
group_by_at(vars(trait, GroupingTerm)) %>%
filter(sig == 1) %>%
summarise(male_sig = sum(value > 0), female_sig = sum(value < 0), total = male_sig + female_sig)
meta.plotS2.sig.malebias <- ungroup(meta.plotS2.sig.malebias) %>%
add_row(trait = "lnCVR", GroupingTerm = "Hearing", male_sig = 0, female_sig = 0, .before = 4) %>% # add "Hearing" for lnCVR (not filtered as only zeros)
mutate(malepercent = male_sig * 100 / total, femalepercent = female_sig * 100 / total)
meta.plotS2.sig.malebias$label <- "CI not overlapping zero"
# restructure to create stacked bar plots
meta.plotS2.sig.bothsexes <- as.data.frame(meta.plotS2.sig.malebias)
meta.plotS2.sig.bothsexes.b <- gather(meta.plotS2.sig.bothsexes, key = sex, value = percent, malepercent:femalepercent, factor_key = TRUE)
# create new sample size variable
meta.plotS2.sig.bothsexes.b$samplesize <- with(meta.plotS2.sig.bothsexes.b, ifelse(sex == "malepercent", male_sig, female_sig))
# *Plot Fig2 all significant results (CI not overlapping zero):
# no sig. lnCVR for 'Hearing' in either sex; no sig. male-biased lnCVR for 'Immunology' and 'Eye, and no sig. male-biased lnVR for 'Eye'
malebias_FigS2_sigtraits <-
ggplot(meta.plotS2.sig.bothsexes.b) +
aes(x = GroupingTerm, y = percent, fill = sex) +
geom_col() +
geom_hline(yintercept = 50, linetype = "dashed", color = "gray40") +
geom_text(
data = subset(meta.plotS2.sig.bothsexes.b, samplesize != 0), aes(label = samplesize), position = position_stack(vjust = .5),
color = "white", size = 3.5
) +
facet_grid(
cols = vars(trait), rows = vars(label), labeller = label_wrap_gen(width = 18),
scales = "free", space = "free"
) +
scale_fill_brewer(palette = "Set2") +
theme_bw(base_size = 18) +
theme(
strip.text.y = element_text(angle = 270, size = 10, margin = margin(t = 15, r = 15, b = 15, l = 15)),
strip.text.x = element_text(size = 12),
strip.background = element_rect(colour = NULL, linetype = "blank", fill = "gray90"),
text = element_text(size = 14),
panel.spacing = unit(0.5, "lines"),
panel.border = element_blank(),
axis.line = element_line(),
panel.grid.major.x = element_line(linetype = "solid", colour = "gray95"),
panel.grid.major.y = element_line(linetype = "solid", color = "gray95"),
panel.grid.minor.y = element_blank(),
panel.grid.minor.x = element_blank(),
legend.position = "none",
axis.title.x = element_blank(),
axis.title.y = element_blank()
) +
coord_flip()
# malebias_FigS2_sigtraits # this is Figure S2 APrepare data for traits with effect size ratios > 10% larger in males
meta.plotS2.over10 <- meta_clean %>%
select(lnCVR, lnVR, lnRR, GroupingTerm) %>%
arrange(GroupingTerm)
meta.plotS2.over10.b <- gather(meta.plotS2.over10, trait, value, c(lnCVR, lnVR, lnRR))
meta.plotS2.over10.b$trait <- factor(meta.plotS2.over10.b$trait, levels = c("lnCVR", "lnVR", "lnRR"))
meta.plotS2.over10.c <- meta.plotS2.over10.b %>%
group_by_at(vars(trait, GroupingTerm)) %>%
summarise(
malebias = sum(value > log(11 / 10)), femalebias = sum(value < log(9 / 10)), total = malebias + femalebias,
malepercent = malebias * 100 / total, femalepercent = femalebias * 100 / total
)
meta.plotS2.over10.c$label <- "Sex difference in m/f ratios > 10%"
# restructure to create stacked bar plots
meta.plotS2.over10.c <- as.data.frame(meta.plotS2.over10.c)
meta.plotS2.over10.d <- gather(meta.plotS2.over10.c, key = sex, value = percent, malepercent:femalepercent, factor_key = TRUE)
# create new sample size variable
meta.plotS2.over10.d$samplesize <- with(meta.plotS2.over10.d, ifelse(sex == "malepercent", malebias, femalebias))
# *Plot FigS2 Sex difference in m/f ratio > 10%
malebias_FigS2_over10 <-
ggplot(meta.plotS2.over10.d) +
aes(x = GroupingTerm, y = percent, fill = sex) +
geom_col() +
geom_hline(yintercept = 50, linetype = "dashed", color = "gray40") +
geom_text(
data = subset(meta.plot2.over10.d, samplesize != 0), aes(label = samplesize), position = position_stack(vjust = .5),
color = "white", size = 3.5
) +
facet_grid(
cols = vars(trait), rows = vars(label), labeller = label_wrap_gen(width = 18),
scales = "free", space = "free"
) +
scale_fill_brewer(palette = "Set2") +
theme_bw(base_size = 18) +
theme(
strip.text.y = element_text(angle = 270, size = 10, margin = margin(t = 15, r = 15, b = 15, l = 15)),
strip.text.x = element_blank(),
strip.background = element_rect(colour = NULL, linetype = "blank", fill = "gray90"),
text = element_text(size = 14),
panel.spacing = unit(0.5, "lines"),
panel.border = element_blank(),
axis.line = element_line(),
panel.grid.major.x = element_line(linetype = "solid", colour = "gray95"),
panel.grid.major.y = element_line(linetype = "solid", color = "gray95"),
panel.grid.minor.y = element_blank(),
panel.grid.minor.x = element_blank(),
legend.position = "none",
axis.title.x = element_blank(),
axis.title.y = element_blank()
) +
coord_flip()
# malebias_FigS2_over10 #(Panel B in Fig S2 in ms)Female FigS2 B sig
Prepare data for traits with CI not overlapping 0 create column with 1= different from zero, 0= zero included in CI
Restructure data for plotting
overall3.female.sigS <- gather(overall.female.plot3, parameter, value, c(lnCVR, lnVR, lnRR), factor_key = TRUE)
lnCVR.ci <- overall3.female.sigS %>%
filter(parameter == "lnCVR") %>%
mutate(ci.low = lnCVR_lower, ci.high = lnCVR_upper)
lnVR.ci <- overall3.female.sigS %>%
filter(parameter == "lnVR") %>%
mutate(ci.low = lnVR_lower, ci.high = lnVR_upper)
lnRR.ci <- overall3.female.sigS %>%
filter(parameter == "lnRR") %>%
mutate(ci.low = lnRR_lower, ci.high = lnRR_upper)
overall4.female.sigS <- bind_rows(lnCVR.ci, lnVR.ci, lnRR.ci) %>% select(GroupingTerm, parameter, value, ci.low, ci.high)
overall4.female.sigS$label <- "CI not overlapping zero"
##
Metameta_FigS2_female.sig <- overall4.female.sigS %>%
ggplot(aes(y = GroupingTerm, x = value)) +
geom_errorbarh(aes(
xmin = ci.low,
xmax = ci.high
),
height = 0.1, show.legend = FALSE
) +
geom_point(aes(shape = parameter),
fill = "salmon1", color = "salmon1", size = 2.2,
show.legend = FALSE
) +
scale_x_continuous(
limits = c(-0.4, 0),
breaks = c(-0.3, 0),
name = "Effect size"
) +
geom_vline(
xintercept = 0,
color = "black",
linetype = "dashed"
) +
facet_grid(
cols = vars(parameter), # rows = vars(label),
# labeller = label_wrap_gen(width = 23),
scales = "free",
space = "free"
) +
theme_bw() +
theme(
strip.text.y = element_text(angle = 270, size = 10, margin = margin(t = 15, r = 15, b = 15, l = 15)),
strip.text.x = element_text(size = 12),
strip.background = element_rect(colour = NULL, linetype = "blank", fill = "gray90"),
text = element_text(size = 14),
panel.spacing = unit(0.5, "lines"),
panel.border = element_blank(),
axis.line = element_line(),
panel.grid.major.x = element_line(linetype = "solid", colour = "gray95"),
panel.grid.major.y = element_line(linetype = "solid", color = "gray95"),
panel.grid.minor.y = element_blank(),
panel.grid.minor.x = element_blank(),
legend.title = element_blank(),
axis.title.x = element_blank(),
axis.title.y = element_blank()
)
# Metameta_FigS2_female.sig#Metameta_FigS2_male.sig (Figure 5B right panel)
Restructure MALE data for plotting
overall3.male.sigS <- gather(overall.male.plot3, parameter, value, c(lnCVR, lnVR, lnRR), factor_key = TRUE)
lnCVR.ci <- overall3.male.sigS %>%
filter(parameter == "lnCVR") %>%
mutate(ci.low = lnCVR_lower, ci.high = lnCVR_upper)
lnVR.ci <- overall3.male.sigS %>%
filter(parameter == "lnVR") %>%
mutate(ci.low = lnVR_lower, ci.high = lnVR_upper)
lnRR.ci <- overall3.male.sigS %>%
filter(parameter == "lnRR") %>%
mutate(ci.low = lnRR_lower, ci.high = lnRR_upper)
overall4.male.sigS <- bind_rows(lnCVR.ci, lnVR.ci, lnRR.ci) %>% select(GroupingTerm, parameter, value, ci.low, ci.high)
overall4.male.sigS$label <- "CI not overlapping zero"Plot FigS2 all significant results (CI not overlapping zero, male )
Metameta_FigS2_male.sig <- overall4.male.sigS %>%
ggplot(aes(y = GroupingTerm, x = value)) +
geom_errorbarh(aes(
xmin = ci.low,
xmax = ci.high
),
height = 0.1, show.legend = FALSE
) +
geom_point(aes(shape = parameter),
fill = "mediumaquamarine", color = "mediumaquamarine", size = 2.2,
show.legend = FALSE
) +
scale_x_continuous(
limits = c(0, 0.4),
breaks = c(0, 0.3),
name = "Effect size"
) +
geom_vline(
xintercept = 0,
color = "black",
linetype = "dashed"
) +
facet_grid(
cols = vars(parameter), rows = vars(label),
labeller = label_wrap_gen(width = 23),
scales = "free",
space = "free"
) +
theme_bw() +
theme(
strip.text.y = element_text(angle = 270, size = 10, margin = margin(t = 15, r = 15, b = 15, l = 15)),
strip.text.x = element_text(size = 12),
strip.background = element_rect(colour = NULL, linetype = "blank", fill = "gray90"),
text = element_text(size = 14),
panel.spacing = unit(0.5, "lines"),
panel.border = element_blank(),
axis.line = element_line(),
panel.grid.major.x = element_line(linetype = "solid", colour = "gray95"),
panel.grid.major.y = element_line(linetype = "solid", color = "gray95"),
panel.grid.minor.y = element_blank(),
panel.grid.minor.x = element_blank(),
legend.title = element_blank(),
axis.title.x = element_blank(),
axis.title.y = element_blank()
)
# Metameta_FigS2_male.sigRestructure data for plotting : Male biased, 10% difference
overall3S.perc <- gather(overall.male.plot3.perc, parameter, value, c(lnCVR, lnVR, lnRR), factor_key = TRUE) # lnVR,
lnCVR.ci <- overall3S.perc %>%
filter(parameter == "lnCVR") %>%
mutate(ci.low = lnCVR_lower, ci.high = lnCVR_upper)
lnVR.ci <- overall3S.perc %>%
filter(parameter == "lnVR") %>%
mutate(ci.low = lnVR_lower, ci.high = lnVR_upper)
lnRR.ci <- overall3S.perc %>%
filter(parameter == "lnRR") %>%
mutate(ci.low = lnRR_lower, ci.high = lnRR_upper)
overall4S.male.perc <- bind_rows(lnCVR.ci, lnVR.ci, lnRR.ci) %>% select(GroupingTerm, parameter, value, ci.low, ci.high) # lnVR.ci,
overall4S.male.perc$label <- "Sex difference in m/f ratios > 10%"
overall4S.male.perc$value <- as.numeric(overall4S.male.perc$value)
overall4S.male.perc$ci.low <- as.numeric(overall4S.male.perc$ci.low)
overall4S.male.perc$ci.high <- as.numeric(overall4S.male.perc$ci.high)Plot FigS2 all >10% difference (male bias)
Metameta_FigS2_male.perc <- overall4S.male.perc %>% # filter(., GroupingTerm != "Hearing") %>%
ggplot(aes(y = GroupingTerm, x = value)) +
geom_errorbarh(aes(
xmin = ci.low,
xmax = ci.high
),
height = 0.1, show.legend = FALSE
) +
geom_point(aes(
shape = parameter,
fill = parameter
),
color = "mediumaquamarine", size = 2.2,
show.legend = FALSE
) +
scale_x_continuous(
limits = c(-0.2, 0.62),
breaks = c(0, 0.3),
name = "Effect size"
) +
geom_vline(
xintercept = 0,
color = "black",
linetype = "dashed"
) +
facet_grid(
cols = vars(parameter), rows = vars(label),
labeller = label_wrap_gen(width = 23),
scales = "free",
space = "free"
) +
theme_bw() +
theme(
strip.text.y = element_text(angle = 270, size = 10, margin = margin(t = 15, r = 15, b = 15, l = 15)),
strip.text.x = element_blank(),
strip.background = element_rect(colour = NULL, linetype = "blank", fill = "gray90"),
text = element_text(size = 14),
panel.spacing = unit(0.5, "lines"),
panel.border = element_blank(),
axis.line = element_line(),
panel.grid.major.x = element_line(linetype = "solid", colour = "gray95"),
panel.grid.major.y = element_line(linetype = "solid", color = "gray95"),
panel.grid.minor.y = element_blank(),
panel.grid.minor.x = element_blank(),
legend.title = element_blank(),
axis.title.x = element_text(hjust = 0.5, size = 14),
axis.title.y = element_blank()
)
# Metameta_FigS2_male.perc (Figure 5D right panel)Restructure data for plotting: Female bias, 10 percent difference, including VR
overall3S.perc <- gather(overall.plot3.perc, parameter, value, c(lnCVR, lnVR, lnRR), factor_key = TRUE) # lnVR,
lnCVR.ci <- overall3S.perc %>%
filter(parameter == "lnCVR") %>%
mutate(ci.low = lnCVR_lower, ci.high = lnCVR_upper)
lnVR.ci <- overall3S.perc %>%
filter(parameter == "lnVR") %>%
mutate(ci.low = lnVR_lower, ci.high = lnVR_upper)
lnRR.ci <- overall3S.perc %>%
filter(parameter == "lnRR") %>%
mutate(ci.low = lnRR_lower, ci.high = lnRR_upper)
overall4S.perc <- bind_rows(lnCVR.ci, lnVR.ci, lnRR.ci) %>% select(GroupingTerm, parameter, value, ci.low, ci.high)
overall4S.perc$label <- "Sex difference in m/f ratios > 10%"
overall4S.perc$value <- as.numeric(overall4S.perc$value)
overall4S.perc$ci.low <- as.numeric(overall4S.perc$ci.low)
overall4S.perc$ci.high <- as.numeric(overall4S.perc$ci.high)Plot Fig5D all >10% difference (female)
Metameta_Fig3S_female.perc <- overall4S.perc %>%
ggplot(aes(y = GroupingTerm, x = value)) +
geom_errorbarh(aes(
xmin = ci.low,
xmax = ci.high
),
height = 0.1, show.legend = FALSE
) +
geom_point(aes(shape = parameter),
fill = "salmon1", color = "salmon1", size = 2.2,
show.legend = FALSE
) +
# scale_shape_manual(values =
scale_x_continuous(
limits = c(-0.53, 0.2),
breaks = c(-0.3, 0),
name = "Effect size"
) +
geom_vline(
xintercept = 0,
color = "black",
linetype = "dashed"
) +
facet_grid(
cols = vars(parameter), # rows = vars(label),
# labeller = label_wrap_gen(width = 23),
scales = "free",
space = "free"
) +
theme_bw() +
theme(
strip.text.y = element_text(angle = 270, size = 10, margin = margin(t = 15, r = 15, b = 15, l = 15)),
strip.text.x = element_blank(),
strip.background = element_rect(colour = NULL, linetype = "blank", fill = "gray90"),
text = element_text(size = 14),
panel.spacing = unit(0.5, "lines"),
panel.border = element_blank(),
axis.line = element_line(),
panel.grid.major.x = element_line(linetype = "solid", colour = "gray95"),
panel.grid.major.y = element_line(linetype = "solid", color = "gray95"),
panel.grid.minor.y = element_blank(),
panel.grid.minor.x = element_blank(),
legend.title = element_blank(),
axis.title.x = element_text(hjust = 0.5, size = 14),
axis.title.y = element_blank()
)
# Metameta_Fig3S_female.perc (Figure 5D left panel)Figure S2
FigS2c <- ggarrange(Metameta_FigS2_female.sig, Metameta_FigS2_male.sig,
ncol = 2, nrow = 1, widths = c(1, 1.20), heights = c(1, 1)
)
FigS2d <- ggarrange(Metameta_Fig3S_female.perc, Metameta_FigS2_male.perc,
ncol = 2, nrow = 1, widths = c(1, 1.20), heights = c(1, 1)
)
# end combination Figure 5
FigS2 <- ggarrange(malebias_FigS2_sigtraits, malebias_FigS2_over10, FigS2c, FigS2d, ncol = 1, nrow = 4, heights = c(2.2, 2, 2.2, 2), labels = c("A", " ", "B", " "))
FigS2tbd
sessionInfo()