R/GenerateFigure/demographic_confounder_figures.R
In arytontediarjo/mPowerRerun: MPower Study Rerun
Defines functions
main
CompareCorVsdCorFigure
GeneratePatternFigure
AdjustPvals
###################################################
#' This script is used to generate supplementary figure
#' 14 to 31 of the mPower Paper
#' It will graph demographic confounders
#' for age, gender, education
#' @author: Elias Chaibub Neto, Aryton Tediarjo
#' @author_email: echaibub@synapse.org, aryton.tediarjo@sagebase.org
##################################################
library(synapser)
library(config)
library(tidyverse)
library(dplyr)
library(jsonlite)
library(githubr)
library(rhdf5)
source("R/utils/projectUtils.R")
source("R/utils/initializeVariables.R")
######################################################
## Configuration
#######################################################
synLogin()
config::get()
setGithubToken(
readLines(get("git")$path))
######################################################
## Variables and Synapse References
#######################################################
SYN_ID_REF <- list(figures = get_figure_ref(),
intermediate = get_intermediate_data_ref())
SCRIPT_NAME <- "demographic_confounder_figures.R"
GIT_URL <- getPermlink(getRepo(get("git")$repo,
ref="branch",
refName=get("git")$branch),
repositoryPath = file.path("R/GenerateFigure", SCRIPT_NAME))
FIGURE_OUTPUT_SYN_ID <- SYN_ID_REF$figures$output_folder
CORR_TBL_SYN_ID <- SYN_ID_REF$intermediate$confounder_corr
DCORR_TBL_SYN_ID <- SYN_ID_REF$intermediate$confounder_dcorr
ANNOTATIONS <- list(analysisType = "demographics confounders",
userSubset = tolower(get("metadata")$user_group),
pipelineStep = "figures")
AdjustPvals <- function(x, method = "bonf") {
-log10(apply(x, 2, p.adjust, method))
}
GeneratePatternFigure <- function(tapD, walD, resD, voiD,
plottitle = "",
cexleg = 1.2,
cext1 = 1.2,
cext2 = 1.5,
titlePos = -0.5,
mylim = c(0.3, 0.7)) {
# figure parameter
colorTap <- "#00A087FF"
colorVoi <- "#7E6148FF"
colorWal <- "#E64B36FF"
colorRes <- "#8491B4FF"
cexleg <- 1.2
mylim <- c(-0.3, 0.7)
figpath <- ""
idx1 <- 1:5
idx2 <- 6:10
colnames(tapD) <- rep(c("cor(R,Y)", "cor(R,A)", "cor(A,Y)", "cor(R,Y|A)", "cor(R,A|Y)"), 2)
colnames(walD) <- rep(c("cor(R,Y)", "cor(R,A)", "cor(A,Y)", "cor(R,Y|A)", "cor(R,A|Y)"), 2)
colnames(resD) <- rep(c("cor(R,Y)", "cor(R,A)", "cor(A,Y)", "cor(R,Y|A)", "cor(R,A|Y)"), 2)
colnames(voiD) <- rep(c("cor(R,Y)", "cor(R,A)", "cor(A,Y)", "cor(R,Y|A)", "cor(R,A|Y)"), 2)
par(mfrow = c(2, 4), mar = c(0.1, 3.0, 5.5, 0.5), mgp = c(2.0, 0.75, 0))
#### a
boxplot(tapD[, idx1], las = 2, ylim = mylim, main = "",
ylab = "correlation",
col = "white",
border = colorTap,
xaxt = "n")
mtext(side = 3, "tapping",
cex = cext1,
line = 0.1)
abline(h = 0, col = "grey")
legend("topright", legend = "(a)", cex = cexleg, bty = "n")
#### b
boxplot(walD[, idx1], las = 2,
ylim = mylim, main = "",
ylab = "correlation",
border = colorWal,
xaxt = "n",
col = "white")
mtext(side = 3, "walk", cex = cext1, line = 0.1)
abline(h = 0, col = "grey")
legend("topright",
legend = "(b)",
cex = cexleg, bty = "n")
### c
boxplot(resD[, idx1], las = 2,
ylim = mylim, main = "",
ylab = "correlation",
col = "white",
border = colorRes, xaxt = "n")
mtext(side = 3, "balance", cex = cext1, line = 0.1)
mtext(side = 3, plottitle, cex = cext2, line = 3, at = titlePos)
abline(h = 0, col = "grey")
legend("topright", legend = "(c)", cex = cexleg, bty = "n")
### d
boxplot(voiD[, idx1], las = 2,
col = "white",
ylim = mylim, main = "",
ylab = "correlation",
border = colorVoi, xaxt = "n")
mtext(side = 3, "voice", cex = cext1, line = 0.1)
abline(h = 0, col = "grey")
legend("topright", legend = "(d)", cex = cexleg, bty = "n")
####
par(mar = c(5.5, 3.0, 0.1, 0.5), mgp = c(2.0, 0.75, 0))
####
mtm <- "BH"
aux <- tapD[, idx2]
aux[aux == 0] <- 1e-323
apvals <- AdjustPvals(aux, mtm)
maxlim <- max(apvals, na.rm = TRUE)
### e
boxplot(apvals,
las = 2,
col = "white",
ylim = c(0, maxlim+1),
main = "",
ylab = "-log10(adjusted p-value)",
border = colorTap)
abline(h = -log10(0.05), col = "red")
legend("topright", legend = "(e)", cex = cexleg, bty = "n")
#
aux <- walD[, idx2]
aux[aux == 0] <- 1e-323
apvals <- AdjustPvals(aux, mtm)
maxlim <- max(apvals, na.rm = TRUE)
### e
boxplot(apvals, las = 2,
ylim = c(0, maxlim+1),
main = "",
col = "white",
ylab = "-log10(adjusted p-value)",
border = colorWal)
abline(h = -log10(0.05), col = "red")
legend("topright", legend = "(f)", cex = cexleg, bty = "n")
#
aux <- resD[, idx2]
aux[aux == 0] <- 1e-323
apvals <- AdjustPvals(aux, mtm)
maxlim <- max(apvals, na.rm = TRUE)
### f
boxplot(apvals, las = 2,
ylim = c(0, maxlim+1),
main = "",
col = "white",
ylab = "-log10(adjusted p-value)",
border = colorRes)
abline(h = -log10(0.05), col = "red")
legend("topright", legend = "(g)", cex = cexleg, bty = "n")
#
aux <- voiD[, idx2]
aux[aux == 0] <- 1e-323
apvals <- AdjustPvals(aux, mtm)
maxlim <- max(apvals, na.rm = TRUE)
### g
boxplot(apvals, las = 2,
ylim = c(0, maxlim+1),
main = "",
col = "white",
ylab = "-log10(adjusted p-value)",
border = colorVoi)
abline(h = -log10(0.05), col = "red")
legend("topright", legend = "(h)", cex = cexleg, bty = "n")
}
CompareCorVsdCorFigure <- function(tapCor,
walCor,
resCor,
voiCor,
tapdCor,
waldCor,
resdCor,
voidCor,
plottitle = "",
cexleg = 1.2,
cext1 = 1.2,
cext2 = 1.5,
titlePos = -0.5) {
# figure parameter
colorTap <- "#00A087FF"
colorVoi <- "#7E6148FF"
colorWal <- "#E64B36FF"
colorRes <- "#8491B4FF"
cexleg <- 1.2
mylim <- c(-0.3, 0.7)
figpath <- ""
idx2 <- 6:10
mtm <- "BH"
par(mfrow = c(2, 4), mar = c(0.1, 3.0, 5.5, 0.5), mgp = c(2.0, 0.75, 0))
####
apvals <- AdjustPvals(tapCor[, idx2], mtm)
maxlim <- max(apvals, na.rm = TRUE)
boxplot(apvals, las = 2,
col = "white",
ylim = c(0, maxlim+1),
main = "",
ylab = "-log10(adjusted p-value)",
border = colorTap,
xaxt = "n")
mtext(side = 3, "tapping", cex = cext1, line = 0.1)
abline(h = -log10(0.05), col = "red")
legend("topright", legend = "(a)", cex = cexleg, bty = "n")
#
apvals <- AdjustPvals(walCor[, idx2], mtm)
maxlim <- max(apvals, na.rm = TRUE)
boxplot(apvals,
col = "white",
las = 2,
ylim = c(0, maxlim+1),
main = "",
ylab = "-log10(adjusted p-value)",
border = colorWal, xaxt = "n")
mtext(side = 3, "walk", cex = cext1, line = 0.1)
abline(h = -log10(0.05), col = "red")
legend("topright", legend = "(b)", cex = cexleg, bty = "n")
#
apvals <- AdjustPvals(resCor[, idx2], mtm)
maxlim <- max(apvals, na.rm = TRUE)
boxplot(apvals,
col = "white",
las = 2,
ylim = c(0, maxlim+1),
main = "",
ylab = "-log10(adjusted p-value)",
border = colorRes, xaxt = "n")
mtext(side = 3, "balance", cex = cext1, line = 0.1)
mtext(side = 3, plottitle, cex = cext2, line = 3, at = titlePos)
abline(h = -log10(0.05), col = "red")
legend("topright", legend = "(c)", cex = cexleg, bty = "n")
#
apvals <- AdjustPvals(voiCor[, idx2], mtm)
maxlim <- max(apvals, na.rm = TRUE)
boxplot(apvals, col = "white",
las = 2,
ylim = c(0, maxlim+1),
main = "",
ylab = "-log10(adjusted p-value)",
border = colorVoi, xaxt = "n")
mtext(side = 3, "voice", cex = cext1, line = 0.1)
abline(h = -log10(0.05), col = "red")
legend("topright", legend = "(d)", cex = cexleg, bty = "n")
####
par(mar = c(5.5, 3.0, 0.1, 0.5), mgp = c(2.0, 0.75, 0))
####
apvals <- AdjustPvals(tapdCor[, idx2], mtm)
maxlim <- max(apvals, na.rm = TRUE)
boxplot(apvals,
col = "white",
las = 2,
ylim = c(0, maxlim+1),
main = "",
ylab = "-log10(adjusted p-value)",
border = colorTap)
abline(h = -log10(0.05), col = "red")
legend("topright", legend = "(e)", cex = cexleg, bty = "n")
#
apvals <- AdjustPvals(waldCor[, idx2], mtm)
maxlim <- max(apvals, na.rm = TRUE)
boxplot(apvals,
col = "white",
las = 2,
ylim = c(0, maxlim+1),
main = "",
ylab = "-log10(adjusted p-value)",
border = colorWal)
abline(h = -log10(0.05), col = "red")
legend("topright", legend = "(f)", cex = cexleg, bty = "n")
#
apvals <- AdjustPvals(resdCor[, idx2], mtm)
maxlim <- max(apvals, na.rm = TRUE)
boxplot(apvals,
col = "white",
las = 2,
ylim = c(0, maxlim+1),
main = "",
ylab = "-log10(adjusted p-value)",
border = colorRes)
abline(h = -log10(0.05), col = "red")
legend("topright", legend = "(g)", cex = cexleg, bty = "n")
#
apvals <- AdjustPvals(voidCor[, idx2], mtm)
maxlim <- max(apvals, na.rm = TRUE)
boxplot(apvals,
col = "white",
las = 2,
ylim = c(0, maxlim+1),
main = "",
ylab = "-log10(adjusted p-value)",
border = colorVoi)
abline(h = -log10(0.05), col = "red")
legend("topright", legend = "(h)", cex = cexleg, bty = "n")
}
main <- function(){
#######################################################
## read table
#######################################################
corr_tbl <- H5Fopen(synGet(CORR_TBL_SYN_ID)$path)
dcorr_tbl <- H5Fopen(synGet(DCORR_TBL_SYN_ID)$path)
dcorr_tbl1 <- H5Fopen(synGet(DCORR_TBL_SYN_ID)$path)
#######################################################
## Random Forest Figures
#######################################################
title <- paste0("mPower_",
gsub(" ", "_", get("metadata")$user_group),
"_supplementary_figure_14",".png")
png(title, width = 2100, height = 1300, res = 200)
GeneratePatternFigure(tapD = h5read(corr_tbl, "tap/age_rf/corRf"),
walD = h5read(corr_tbl, "walk/age_rf/corRf"),
resD = h5read(corr_tbl, "rest/age_rf/corRf"),
voiD = h5read(corr_tbl, "voice/age_rf/corRf"),
plottitle = "age - unmatched - random forest",
cext2 = 1.7,
mylim = mylim)
dev.off()
f <- synapser::File(title, parent=FIGURE_OUTPUT_SYN_ID)
f$annotations <- ANNOTATIONS
synStore(f, activity = Activity(
"generate confounder figure",
executed = GIT_URL,
used = c(CORR_TBL_SYN_ID, DCORR_TBL_SYN_ID)))
unlink(title)
## umatched gender ##
title <- paste0("mPower_",
gsub(" ", "_", get("metadata")$user_group),
"_supplementary_figure_15",".png")
png(title, width = 2100, height = 1300, res = 200)
GeneratePatternFigure(tapD = h5read(corr_tbl, "tap/gender_rf/corRf"),
walD = h5read(corr_tbl, "walk/gender_rf/corRf"),
resD = h5read(corr_tbl, "rest/gender_rf/corRf"),
voiD = h5read(corr_tbl, "voice/gender_rf/corRf"),
plottitle = "gender - unmatched - random forest",
cext2 = 1.7,
mylim = mylim)
dev.off()
f <- synapser::File(title, parent=FIGURE_OUTPUT_SYN_ID)
f$annotations <- ANNOTATIONS
synStore(f, activity = Activity(
"generate confounder figure",
executed = GIT_URL,
used = c(CORR_TBL_SYN_ID, DCORR_TBL_SYN_ID)))
unlink(title)
## umatched education ##
title <- paste0("mPower_",
gsub(" ", "_", get("metadata")$user_group),
"_supplementary_figure_16",".png")
png(title, width = 2100, height = 1300, res = 200)
GeneratePatternFigure(tapD = h5read(corr_tbl, "tap/education_rf/corRf"),
walD = h5read(corr_tbl, "walk/education_rf/corRf"),
resD = h5read(corr_tbl, "rest/education_rf/corRf"),
voiD = h5read(corr_tbl, "voice/education_rf/corRf"),
plottitle = "education - unmatched - random forest",
cext2 = 1.7,
mylim = mylim)
dev.off()
f <- synapser::File(title, parent=FIGURE_OUTPUT_SYN_ID)
f$annotations <- ANNOTATIONS
synStore(f, activity = Activity(
"generate confounder figure",
executed = GIT_URL,
used = c(CORR_TBL_SYN_ID, DCORR_TBL_SYN_ID)))
unlink(title)
##############################
## Ridge Regression Figures
##############################
## unmatched age ##
title <- paste0("mPower_",
gsub(" ", "_", get("metadata")$user_group),
"_supplementary_figure_17",".png")
png(title, width = 2100, height = 1300, res = 200)
GeneratePatternFigure(tapD = h5read(corr_tbl, "tap/age_rr/corRr"),
walD = h5read(corr_tbl, "walk/age_rr/corRr"),
resD = h5read(corr_tbl, "rest/age_rr/corRr"),
voiD = h5read(corr_tbl, "voice/age_rr/corRr"),
plottitle = "age - unmatched - ridge regression",
cext2 = 1.7,
mylim = mylim)
dev.off()
f <- synapser::File(title, parent=FIGURE_OUTPUT_SYN_ID)
f$annotations <- ANNOTATIONS
synStore(f, activity = Activity(
"generate confounder figure",
executed = GIT_URL,
used = c(CORR_TBL_SYN_ID, DCORR_TBL_SYN_ID)))
unlink(title)
## umatched gender ##
title <- paste0("mPower_",
gsub(" ", "_", get("metadata")$user_group),
"_supplementary_figure_18",".png")
png(title, width = 2100, height = 1300, res = 200)
GeneratePatternFigure(tapD = h5read(corr_tbl, "tap/gender_rr/corRr"),
walD = h5read(corr_tbl, "walk/gender_rr/corRr"),
resD = h5read(corr_tbl, "rest/gender_rr/corRr"),
voiD = h5read(corr_tbl, "voice/gender_rr/corRr"),
plottitle = "gender - unmatched - ridge regression",
cext2 = 1.7,
mylim = mylim)
dev.off()
f <- synapser::File(title, parent=FIGURE_OUTPUT_SYN_ID)
f$annotations <- ANNOTATIONS
synStore(f, activity = Activity(
"generate confounder figure",
executed = GIT_URL,
used = c(CORR_TBL_SYN_ID, DCORR_TBL_SYN_ID)))
unlink(title)
## umatched education ##
title <- paste0("mPower_",
gsub(" ", "_", get("metadata")$user_group),
"_supplementary_figure_19",".png")
png(title, width = 2100, height = 1300, res = 200)
GeneratePatternFigure(tapD = h5read(corr_tbl, "tap/education_rr/corRr"),
walD = h5read(corr_tbl, "walk/education_rr/corRr"),
resD = h5read(corr_tbl, "rest/education_rr/corRr"),
voiD = h5read(corr_tbl, "voice/education_rr/corRr"),
plottitle = "education - unmatched - ridge regression",
cext2 = 1.7,
mylim = mylim)
dev.off()
f <- synapser::File(title, parent=FIGURE_OUTPUT_SYN_ID)
f$annotations <- ANNOTATIONS
synStore(f, activity = Activity(
"generate confounder figure",
executed = GIT_URL,
used = c(CORR_TBL_SYN_ID, DCORR_TBL_SYN_ID)))
unlink(title)
## matched age ##
title <- paste0("mPower_",
gsub(" ", "_", get("metadata")$user_group),
"_supplementary_figure_20",".png")
png(title, width = 2100, height = 1300, res = 200)
GeneratePatternFigure(tapD = h5read(corr_tbl, "tap/age_rf/corRfM"),
walD = h5read(corr_tbl, "walk/age_rf/corRfM"),
resD = h5read(corr_tbl, "rest/age_rf/corRfM"),
voiD = h5read(corr_tbl, "voice/age_rf/corRfM"),
plottitle = "age - matched - random forest",
cext2 = 1.7,
mylim = mylim)
dev.off()
f <- synapser::File(title, parent=FIGURE_OUTPUT_SYN_ID)
f$annotations <- ANNOTATIONS
synStore(f, activity = Activity(
"generate confounder figure",
executed = GIT_URL,
used = c(CORR_TBL_SYN_ID, DCORR_TBL_SYN_ID)))
unlink(title)
## matched gender ##
title <- paste0("mPower_",
gsub(" ", "_", get("metadata")$user_group),
"_supplementary_figure_21",".png")
png(title, width = 2100, height = 1300, res = 200)
GeneratePatternFigure(tapD = h5read(corr_tbl, "tap/gender_rf/corRfM"),
walD = h5read(corr_tbl, "walk/gender_rf/corRfM"),
resD = h5read(corr_tbl, "rest/gender_rf/corRfM"),
voiD = h5read(corr_tbl, "voice/gender_rf/corRfM"),
plottitle = "gender - matched - random forest",
cext2 = 1.7,
mylim = mylim)
dev.off()
f <- synapser::File(title, parent=FIGURE_OUTPUT_SYN_ID)
f$annotations <- ANNOTATIONS
synStore(f, activity = Activity(
"generate demo confounding figure",
executed = GIT_URL, used = c(CORR_TBL_SYN_ID, DCORR_TBL_SYN_ID)))
unlink(title)
## matched education ##
title <- paste0("mPower_",
gsub(" ", "_", get("metadata")$user_group),
"_supplementary_figure_22",".png")
png(title, width = 2100, height = 1300, res = 200)
GeneratePatternFigure(tapD = h5read(corr_tbl, "tap/education_rf/corRfM"),
walD = h5read(corr_tbl, "walk/education_rf/corRfM"),
resD = h5read(corr_tbl, "rest/education_rf/corRfM"),
voiD = h5read(corr_tbl, "voice/education_rf/corRfM"),
plottitle = "education - matched - random forest",
cext2 = 1.7,
mylim = mylim)
dev.off()
f <- synapser::File(title, parent=FIGURE_OUTPUT_SYN_ID)
f$annotations <- ANNOTATIONS
synStore(f, activity = Activity(
"generate confounder figure",
executed = GIT_URL,
used = c(CORR_TBL_SYN_ID, DCORR_TBL_SYN_ID)))
unlink(title)
## matched age ##
title <- paste0("mPower_",
gsub(" ", "_", get("metadata")$user_group),
"_supplementary_figure_23",".png")
png(title, width = 2100, height = 1300, res = 200)
GeneratePatternFigure(tapD = h5read(corr_tbl, "tap/age_rr/corRrM"),
walD = h5read(corr_tbl, "walk/age_rr/corRrM"),
resD = h5read(corr_tbl, "rest/age_rr/corRrM"),
voiD = h5read(corr_tbl, "voice/age_rr/corRrM"),
plottitle = "age - matched - ridge regression",
cext2 = 1.7,
mylim = mylim)
dev.off()
f <- synapser::File(title, parent=FIGURE_OUTPUT_SYN_ID)
f$annotations <- ANNOTATIONS
synStore(f, activity = Activity(
"generate confounder figure",
executed = GIT_URL,
used = c(CORR_TBL_SYN_ID, DCORR_TBL_SYN_ID)))
unlink(title)
## matched gender ##
title <- paste0("mPower_",
gsub(" ", "_", get("metadata")$user_group),
"_supplementary_figure_24",".png")
png(title, width = 2100, height = 1300, res = 200)
GeneratePatternFigure(tapD = h5read(corr_tbl, "tap/gender_rr/corRrM"),
walD = h5read(corr_tbl, "walk/gender_rr/corRrM"),
resD = h5read(corr_tbl, "rest/gender_rr/corRrM"),
voiD = h5read(corr_tbl, "voice/gender_rr/corRrM"),
plottitle = "gender - matched - ridge regression",
cext2 = 1.7,
mylim = mylim)
dev.off()
f <- synapser::File(title, parent=FIGURE_OUTPUT_SYN_ID)
f$annotations <- ANNOTATIONS
synStore(f, activity = Activity(
"generate confounder figure",
executed = GIT_URL,
used = c(CORR_TBL_SYN_ID, DCORR_TBL_SYN_ID)))
unlink(title)
## matched education ##
title <- paste0("mPower_",
gsub(" ", "_", get("metadata")$user_group),
"_supplementary_figure_25",".png")
png(title, width = 2100, height = 1300, res = 200)
GeneratePatternFigure(tapD = h5read(corr_tbl, "tap/education_rr/corRrM"),
walD = h5read(corr_tbl, "walk/education_rr/corRrM"),
resD = h5read(corr_tbl, "rest/education_rr/corRrM"),
voiD = h5read(corr_tbl, "voice/education_rr/corRrM"),
plottitle = "education - matched - ridge regression",
cext2 = 1.7,
mylim = mylim)
dev.off()
f <- synapser::File(title, parent=FIGURE_OUTPUT_SYN_ID)
f$annotations <- ANNOTATIONS
synStore(f, activity = Activity(
"generate confounder figure",
executed = GIT_URL,
used = c(CORR_TBL_SYN_ID, DCORR_TBL_SYN_ID)))
unlink(title)
#################################################
## Compare correlation vs distance correlation
#################################################
title <- paste0("mPower_",
gsub(" ", "_", get("metadata")$user_group),
"_supplementary_figure_26",".png")
png(title, width = 2100, height = 1300, res = 200)
CompareCorVsdCorFigure(tapCor = h5read(corr_tbl, "tap/age_rf/corRfM"),
walCor = h5read(corr_tbl, "walk/age_rf/corRfM"),
resCor = h5read(corr_tbl, "rest/age_rf/corRfM"),
voiCor = h5read(corr_tbl, "voice/age_rf/corRfM"),
tapdCor = h5read(dcorr_tbl, "tap/age_rf/corRf"),
waldCor = h5read(dcorr_tbl, "walk/age_rf/corRf"),
resdCor = h5read(dcorr_tbl, "rest/age_rf/corRf"),
voidCor = h5read(dcorr_tbl, "voice/age_rf/corRf"),
plottitle = "age - cor. vs distance cor. tests - random forest",
cexleg = 1.2,
cext1 = 1.2,
cext2 = 1.7,
titlePos = -0.5)
dev.off()
f <- synapser::File(title, parent=FIGURE_OUTPUT_SYN_ID)
f$annotations <- ANNOTATIONS
synStore(f, activity = Activity(
"generate confounder figure",
executed = GIT_URL,
used = c(CORR_TBL_SYN_ID, DCORR_TBL_SYN_ID)))
unlink(title)
title <- paste0("mPower_",
gsub(" ", "_", get("metadata")$user_group),
"_supplementary_figure_27",".png")
png(title, width = 2100, height = 1300, res = 200)
CompareCorVsdCorFigure(tapCor = h5read(corr_tbl, "tap/gender_rf/corRfM"),
walCor = h5read(corr_tbl, "walk/gender_rf/corRfM"),
resCor = h5read(corr_tbl, "rest/gender_rf/corRfM"),
voiCor = h5read(corr_tbl, "voice/gender_rf/corRfM"),
tapdCor = h5read(dcorr_tbl, "tap/gender_rf/corRf"),
waldCor = h5read(dcorr_tbl, "walk/gender_rf/corRf"),
resdCor = h5read(dcorr_tbl, "rest/gender_rf/corRf"),
voidCor = h5read(dcorr_tbl, "voice/gender_rf/corRf"),
plottitle = "gender - cor. vs distance cor. tests - random forest",
cexleg = 1.2,
cext1 = 1.2,
cext2 = 1.7,
titlePos = -0.5)
dev.off()
f <- synapser::File(title, parent=FIGURE_OUTPUT_SYN_ID)
f$annotations <- ANNOTATIONS
synStore(f, activity = Activity(
"generate confounder figure",
executed = GIT_URL,
used = c(CORR_TBL_SYN_ID, DCORR_TBL_SYN_ID)))
unlink(title)
title <- paste0("mPower_",
gsub(" ", "_", get("metadata")$user_group),
"_supplementary_figure_28",".png")
png(title, width = 2100, height = 1300, res = 200)
CompareCorVsdCorFigure(tapCor = h5read(corr_tbl, "tap/education_rf/corRfM"),
walCor = h5read(corr_tbl, "walk/education_rf/corRfM"),
resCor = h5read(corr_tbl, "rest/education_rf/corRfM"),
voiCor = h5read(corr_tbl, "voice/education_rf/corRfM"),
tapdCor = h5read(dcorr_tbl, "tap/education_rf/corRf"),
waldCor = h5read(dcorr_tbl, "walk/education_rf/corRf"),
resdCor = h5read(dcorr_tbl, "rest/education_rf/corRf"),
voidCor = h5read(dcorr_tbl, "voice/education_rf/corRf"),
plottitle = "education - cor. vs distance cor. tests - random forest",
cexleg = 1.2,
cext1 = 1.2,
cext2 = 1.7,
titlePos = -0.5)
dev.off()
f <- synapser::File(title, parent=FIGURE_OUTPUT_SYN_ID)
f$annotations <- ANNOTATIONS
synStore(f, activity = Activity(
"generate confounder figure",
executed = GIT_URL,
used = c(CORR_TBL_SYN_ID, DCORR_TBL_SYN_ID)))
unlink(title)
title <- paste0("mPower_",
gsub(" ", "_", get("metadata")$user_group),
"_supplementary_figure_29",".png")
png(title, width = 2100, height = 1300, res = 200)
CompareCorVsdCorFigure(tapCor = h5read(corr_tbl, "tap/age_rr/corRrM"),
walCor = h5read(corr_tbl, "walk/age_rr/corRrM"),
resCor = h5read(corr_tbl, "rest/age_rr/corRrM"),
voiCor = h5read(corr_tbl, "voice/age_rr/corRrM"),
tapdCor = h5read(dcorr_tbl, "tap/age_rr/corRr"),
waldCor = h5read(dcorr_tbl, "walk/age_rr/corRr"),
resdCor = h5read(dcorr_tbl, "rest/age_rr/corRr"),
voidCor = h5read(dcorr_tbl, "voice/age_rr/corRr"),
plottitle = "age - cor. vs distance cor. tests - ridge regression",
cexleg = 1.2,
cext1 = 1.2,
cext2 = 1.7,
titlePos = -0.5)
dev.off()
f <- synapser::File(title, parent=FIGURE_OUTPUT_SYN_ID)
f$annotations <- ANNOTATIONS
synStore(f, activity = Activity(
"generate confounder figure",
executed = GIT_URL,
used = c(CORR_TBL_SYN_ID, DCORR_TBL_SYN_ID)))
unlink(title)
title <- paste0("mPower_",
gsub(" ", "_", get("metadata")$user_group),
"_supplementary_figure_30",".png")
png(title, width = 2100, height = 1300, res = 200)
CompareCorVsdCorFigure(tapCor = h5read(corr_tbl, "tap/gender_rr/corRrM"),
walCor = h5read(corr_tbl, "walk/gender_rr/corRrM"),
resCor = h5read(corr_tbl, "rest/gender_rr/corRrM"),
voiCor = h5read(corr_tbl, "voice/gender_rr/corRrM"),
tapdCor = h5read(dcorr_tbl, "tap/gender_rr/corRr"),
waldCor = h5read(dcorr_tbl, "walk/gender_rr/corRr"),
resdCor = h5read(dcorr_tbl, "rest/gender_rr/corRr"),
voidCor = h5read(dcorr_tbl, "voice/gender_rr/corRr"),
plottitle = "gender - cor. vs distance cor. tests - ridge regression",
cexleg = 1.2,
cext1 = 1.2,
cext2 = 1.7,
titlePos = -0.5)
dev.off()
f <- synapser::File(title, parent=FIGURE_OUTPUT_SYN_ID)
f$annotations <- ANNOTATIONS
synStore(f, activity = Activity(
"generate confounder figure",
executed = GIT_URL,
used = c(CORR_TBL_SYN_ID, DCORR_TBL_SYN_ID)))
unlink(title)
title <- paste0("mPower_",
gsub(" ", "_", get("metadata")$user_group),
"_supplementary_figure_31",".png")
png(title, width = 2100, height = 1300, res = 200)
CompareCorVsdCorFigure(tapCor = h5read(corr_tbl, "tap/education_rr/corRrM"),
walCor = h5read(corr_tbl, "walk/education_rr/corRrM"),
resCor = h5read(corr_tbl, "rest/education_rr/corRrM"),
voiCor = h5read(corr_tbl, "voice/education_rr/corRrM"),
tapdCor = h5read(dcorr_tbl, "tap/education_rr/corRr"),
waldCor = h5read(dcorr_tbl, "walk/education_rr/corRr"),
resdCor = h5read(dcorr_tbl, "rest/education_rr/corRr"),
voidCor = h5read(dcorr_tbl, "voice/education_rr/corRr"),
plottitle = "education - cor. vs distance cor. tests - ridge regression",
cexleg = 1.2,
cext1 = 1.2,
cext2 = 1.7,
titlePos = -0.5)
dev.off()
f <- synapser::File(title, parent=FIGURE_OUTPUT_SYN_ID)
f$annotations <- ANNOTATIONS
synStore(f, activity = Activity(
"generate confounder figure",
executed = GIT_URL,
used = c(CORR_TBL_SYN_ID, DCORR_TBL_SYN_ID)))
unlink(title)
}
tryCatch({
#' create logger for pipeline
sink('pipeline.log', append = TRUE)
cat(paste0(
"[",Sys.time(), "]", " Running ", SCRIPT_NAME), "\n\n")
sink()
#' run script
main()
#' store logger
sink('pipeline.log', append = TRUE)
cat(paste0("[",Sys.time(), "]", " Done Running ", SCRIPT_NAME), "\n\n")
sink()
}, error = function(e) {
sink("error.log")
cat(paste0("[",Sys.time(), "] ", SCRIPT_NAME, " - ", e), "\n\n")
sink()
stop("Stopped due to error - Please check error.log")
})
arytontediarjo/mPowerRerun documentation built on July 23, 2021, 12:04 p.m.
R Package Documentation
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Defines functions main CompareCorVsdCorFigure GeneratePatternFigure AdjustPvals
###################################################
#' This script is used to generate supplementary figure
#' 14 to 31 of the mPower Paper
#' It will graph demographic confounders
#' for age, gender, education
#' @author: Elias Chaibub Neto, Aryton Tediarjo
#' @author_email: echaibub@synapse.org, aryton.tediarjo@sagebase.org
##################################################
library(synapser)
library(config)
library(tidyverse)
library(dplyr)
library(jsonlite)
library(githubr)
library(rhdf5)
source("R/utils/projectUtils.R")
source("R/utils/initializeVariables.R")
######################################################
## Configuration
#######################################################
synLogin()
config::get()
setGithubToken(
readLines(get("git")$path))
######################################################
## Variables and Synapse References
#######################################################
SYN_ID_REF <- list(figures = get_figure_ref(),
intermediate = get_intermediate_data_ref())
SCRIPT_NAME <- "demographic_confounder_figures.R"
GIT_URL <- getPermlink(getRepo(get("git")$repo,
ref="branch",
refName=get("git")$branch),
repositoryPath = file.path("R/GenerateFigure", SCRIPT_NAME))
FIGURE_OUTPUT_SYN_ID <- SYN_ID_REF$figures$output_folder
CORR_TBL_SYN_ID <- SYN_ID_REF$intermediate$confounder_corr
DCORR_TBL_SYN_ID <- SYN_ID_REF$intermediate$confounder_dcorr
ANNOTATIONS <- list(analysisType = "demographics confounders",
userSubset = tolower(get("metadata")$user_group),
pipelineStep = "figures")
AdjustPvals <- function(x, method = "bonf") {
-log10(apply(x, 2, p.adjust, method))
}
GeneratePatternFigure <- function(tapD, walD, resD, voiD,
plottitle = "",
cexleg = 1.2,
cext1 = 1.2,
cext2 = 1.5,
titlePos = -0.5,
mylim = c(0.3, 0.7)) {
# figure parameter
colorTap <- "#00A087FF"
colorVoi <- "#7E6148FF"
colorWal <- "#E64B36FF"
colorRes <- "#8491B4FF"
cexleg <- 1.2
mylim <- c(-0.3, 0.7)
figpath <- ""
idx1 <- 1:5
idx2 <- 6:10
colnames(tapD) <- rep(c("cor(R,Y)", "cor(R,A)", "cor(A,Y)", "cor(R,Y|A)", "cor(R,A|Y)"), 2)
colnames(walD) <- rep(c("cor(R,Y)", "cor(R,A)", "cor(A,Y)", "cor(R,Y|A)", "cor(R,A|Y)"), 2)
colnames(resD) <- rep(c("cor(R,Y)", "cor(R,A)", "cor(A,Y)", "cor(R,Y|A)", "cor(R,A|Y)"), 2)
colnames(voiD) <- rep(c("cor(R,Y)", "cor(R,A)", "cor(A,Y)", "cor(R,Y|A)", "cor(R,A|Y)"), 2)
par(mfrow = c(2, 4), mar = c(0.1, 3.0, 5.5, 0.5), mgp = c(2.0, 0.75, 0))
#### a
boxplot(tapD[, idx1], las = 2, ylim = mylim, main = "",
ylab = "correlation",
col = "white",
border = colorTap,
xaxt = "n")
mtext(side = 3, "tapping",
cex = cext1,
line = 0.1)
abline(h = 0, col = "grey")
legend("topright", legend = "(a)", cex = cexleg, bty = "n")
#### b
boxplot(walD[, idx1], las = 2,
ylim = mylim, main = "",
ylab = "correlation",
border = colorWal,
xaxt = "n",
col = "white")
mtext(side = 3, "walk", cex = cext1, line = 0.1)
abline(h = 0, col = "grey")
legend("topright",
legend = "(b)",
cex = cexleg, bty = "n")
### c
boxplot(resD[, idx1], las = 2,
ylim = mylim, main = "",
ylab = "correlation",
col = "white",
border = colorRes, xaxt = "n")
mtext(side = 3, "balance", cex = cext1, line = 0.1)
mtext(side = 3, plottitle, cex = cext2, line = 3, at = titlePos)
abline(h = 0, col = "grey")
legend("topright", legend = "(c)", cex = cexleg, bty = "n")
### d
boxplot(voiD[, idx1], las = 2,
col = "white",
ylim = mylim, main = "",
ylab = "correlation",
border = colorVoi, xaxt = "n")
mtext(side = 3, "voice", cex = cext1, line = 0.1)
abline(h = 0, col = "grey")
legend("topright", legend = "(d)", cex = cexleg, bty = "n")
####
par(mar = c(5.5, 3.0, 0.1, 0.5), mgp = c(2.0, 0.75, 0))
####
mtm <- "BH"
aux <- tapD[, idx2]
aux[aux == 0] <- 1e-323
apvals <- AdjustPvals(aux, mtm)
maxlim <- max(apvals, na.rm = TRUE)
### e
boxplot(apvals,
las = 2,
col = "white",
ylim = c(0, maxlim+1),
main = "",
ylab = "-log10(adjusted p-value)",
border = colorTap)
abline(h = -log10(0.05), col = "red")
legend("topright", legend = "(e)", cex = cexleg, bty = "n")
#
aux <- walD[, idx2]
aux[aux == 0] <- 1e-323
apvals <- AdjustPvals(aux, mtm)
maxlim <- max(apvals, na.rm = TRUE)
### e
boxplot(apvals, las = 2,
ylim = c(0, maxlim+1),
main = "",
col = "white",
ylab = "-log10(adjusted p-value)",
border = colorWal)
abline(h = -log10(0.05), col = "red")
legend("topright", legend = "(f)", cex = cexleg, bty = "n")
#
aux <- resD[, idx2]
aux[aux == 0] <- 1e-323
apvals <- AdjustPvals(aux, mtm)
maxlim <- max(apvals, na.rm = TRUE)
### f
boxplot(apvals, las = 2,
ylim = c(0, maxlim+1),
main = "",
col = "white",
ylab = "-log10(adjusted p-value)",
border = colorRes)
abline(h = -log10(0.05), col = "red")
legend("topright", legend = "(g)", cex = cexleg, bty = "n")
#
aux <- voiD[, idx2]
aux[aux == 0] <- 1e-323
apvals <- AdjustPvals(aux, mtm)
maxlim <- max(apvals, na.rm = TRUE)
### g
boxplot(apvals, las = 2,
ylim = c(0, maxlim+1),
main = "",
col = "white",
ylab = "-log10(adjusted p-value)",
border = colorVoi)
abline(h = -log10(0.05), col = "red")
legend("topright", legend = "(h)", cex = cexleg, bty = "n")
}
CompareCorVsdCorFigure <- function(tapCor,
walCor,
resCor,
voiCor,
tapdCor,
waldCor,
resdCor,
voidCor,
plottitle = "",
cexleg = 1.2,
cext1 = 1.2,
cext2 = 1.5,
titlePos = -0.5) {
# figure parameter
colorTap <- "#00A087FF"
colorVoi <- "#7E6148FF"
colorWal <- "#E64B36FF"
colorRes <- "#8491B4FF"
cexleg <- 1.2
mylim <- c(-0.3, 0.7)
figpath <- ""
idx2 <- 6:10
mtm <- "BH"
par(mfrow = c(2, 4), mar = c(0.1, 3.0, 5.5, 0.5), mgp = c(2.0, 0.75, 0))
####
apvals <- AdjustPvals(tapCor[, idx2], mtm)
maxlim <- max(apvals, na.rm = TRUE)
boxplot(apvals, las = 2,
col = "white",
ylim = c(0, maxlim+1),
main = "",
ylab = "-log10(adjusted p-value)",
border = colorTap,
xaxt = "n")
mtext(side = 3, "tapping", cex = cext1, line = 0.1)
abline(h = -log10(0.05), col = "red")
legend("topright", legend = "(a)", cex = cexleg, bty = "n")
#
apvals <- AdjustPvals(walCor[, idx2], mtm)
maxlim <- max(apvals, na.rm = TRUE)
boxplot(apvals,
col = "white",
las = 2,
ylim = c(0, maxlim+1),
main = "",
ylab = "-log10(adjusted p-value)",
border = colorWal, xaxt = "n")
mtext(side = 3, "walk", cex = cext1, line = 0.1)
abline(h = -log10(0.05), col = "red")
legend("topright", legend = "(b)", cex = cexleg, bty = "n")
#
apvals <- AdjustPvals(resCor[, idx2], mtm)
maxlim <- max(apvals, na.rm = TRUE)
boxplot(apvals,
col = "white",
las = 2,
ylim = c(0, maxlim+1),
main = "",
ylab = "-log10(adjusted p-value)",
border = colorRes, xaxt = "n")
mtext(side = 3, "balance", cex = cext1, line = 0.1)
mtext(side = 3, plottitle, cex = cext2, line = 3, at = titlePos)
abline(h = -log10(0.05), col = "red")
legend("topright", legend = "(c)", cex = cexleg, bty = "n")
#
apvals <- AdjustPvals(voiCor[, idx2], mtm)
maxlim <- max(apvals, na.rm = TRUE)
boxplot(apvals, col = "white",
las = 2,
ylim = c(0, maxlim+1),
main = "",
ylab = "-log10(adjusted p-value)",
border = colorVoi, xaxt = "n")
mtext(side = 3, "voice", cex = cext1, line = 0.1)
abline(h = -log10(0.05), col = "red")
legend("topright", legend = "(d)", cex = cexleg, bty = "n")
####
par(mar = c(5.5, 3.0, 0.1, 0.5), mgp = c(2.0, 0.75, 0))
####
apvals <- AdjustPvals(tapdCor[, idx2], mtm)
maxlim <- max(apvals, na.rm = TRUE)
boxplot(apvals,
col = "white",
las = 2,
ylim = c(0, maxlim+1),
main = "",
ylab = "-log10(adjusted p-value)",
border = colorTap)
abline(h = -log10(0.05), col = "red")
legend("topright", legend = "(e)", cex = cexleg, bty = "n")
#
apvals <- AdjustPvals(waldCor[, idx2], mtm)
maxlim <- max(apvals, na.rm = TRUE)
boxplot(apvals,
col = "white",
las = 2,
ylim = c(0, maxlim+1),
main = "",
ylab = "-log10(adjusted p-value)",
border = colorWal)
abline(h = -log10(0.05), col = "red")
legend("topright", legend = "(f)", cex = cexleg, bty = "n")
#
apvals <- AdjustPvals(resdCor[, idx2], mtm)
maxlim <- max(apvals, na.rm = TRUE)
boxplot(apvals,
col = "white",
las = 2,
ylim = c(0, maxlim+1),
main = "",
ylab = "-log10(adjusted p-value)",
border = colorRes)
abline(h = -log10(0.05), col = "red")
legend("topright", legend = "(g)", cex = cexleg, bty = "n")
#
apvals <- AdjustPvals(voidCor[, idx2], mtm)
maxlim <- max(apvals, na.rm = TRUE)
boxplot(apvals,
col = "white",
las = 2,
ylim = c(0, maxlim+1),
main = "",
ylab = "-log10(adjusted p-value)",
border = colorVoi)
abline(h = -log10(0.05), col = "red")
legend("topright", legend = "(h)", cex = cexleg, bty = "n")
}
main <- function(){
#######################################################
## read table
#######################################################
corr_tbl <- H5Fopen(synGet(CORR_TBL_SYN_ID)$path)
dcorr_tbl <- H5Fopen(synGet(DCORR_TBL_SYN_ID)$path)
dcorr_tbl1 <- H5Fopen(synGet(DCORR_TBL_SYN_ID)$path)
#######################################################
## Random Forest Figures
#######################################################
title <- paste0("mPower_",
gsub(" ", "_", get("metadata")$user_group),
"_supplementary_figure_14",".png")
png(title, width = 2100, height = 1300, res = 200)
GeneratePatternFigure(tapD = h5read(corr_tbl, "tap/age_rf/corRf"),
walD = h5read(corr_tbl, "walk/age_rf/corRf"),
resD = h5read(corr_tbl, "rest/age_rf/corRf"),
voiD = h5read(corr_tbl, "voice/age_rf/corRf"),
plottitle = "age - unmatched - random forest",
cext2 = 1.7,
mylim = mylim)
dev.off()
f <- synapser::File(title, parent=FIGURE_OUTPUT_SYN_ID)
f$annotations <- ANNOTATIONS
synStore(f, activity = Activity(
"generate confounder figure",
executed = GIT_URL,
used = c(CORR_TBL_SYN_ID, DCORR_TBL_SYN_ID)))
unlink(title)
## umatched gender ##
title <- paste0("mPower_",
gsub(" ", "_", get("metadata")$user_group),
"_supplementary_figure_15",".png")
png(title, width = 2100, height = 1300, res = 200)
GeneratePatternFigure(tapD = h5read(corr_tbl, "tap/gender_rf/corRf"),
walD = h5read(corr_tbl, "walk/gender_rf/corRf"),
resD = h5read(corr_tbl, "rest/gender_rf/corRf"),
voiD = h5read(corr_tbl, "voice/gender_rf/corRf"),
plottitle = "gender - unmatched - random forest",
cext2 = 1.7,
mylim = mylim)
dev.off()
f <- synapser::File(title, parent=FIGURE_OUTPUT_SYN_ID)
f$annotations <- ANNOTATIONS
synStore(f, activity = Activity(
"generate confounder figure",
executed = GIT_URL,
used = c(CORR_TBL_SYN_ID, DCORR_TBL_SYN_ID)))
unlink(title)
## umatched education ##
title <- paste0("mPower_",
gsub(" ", "_", get("metadata")$user_group),
"_supplementary_figure_16",".png")
png(title, width = 2100, height = 1300, res = 200)
GeneratePatternFigure(tapD = h5read(corr_tbl, "tap/education_rf/corRf"),
walD = h5read(corr_tbl, "walk/education_rf/corRf"),
resD = h5read(corr_tbl, "rest/education_rf/corRf"),
voiD = h5read(corr_tbl, "voice/education_rf/corRf"),
plottitle = "education - unmatched - random forest",
cext2 = 1.7,
mylim = mylim)
dev.off()
f <- synapser::File(title, parent=FIGURE_OUTPUT_SYN_ID)
f$annotations <- ANNOTATIONS
synStore(f, activity = Activity(
"generate confounder figure",
executed = GIT_URL,
used = c(CORR_TBL_SYN_ID, DCORR_TBL_SYN_ID)))
unlink(title)
##############################
## Ridge Regression Figures
##############################
## unmatched age ##
title <- paste0("mPower_",
gsub(" ", "_", get("metadata")$user_group),
"_supplementary_figure_17",".png")
png(title, width = 2100, height = 1300, res = 200)
GeneratePatternFigure(tapD = h5read(corr_tbl, "tap/age_rr/corRr"),
walD = h5read(corr_tbl, "walk/age_rr/corRr"),
resD = h5read(corr_tbl, "rest/age_rr/corRr"),
voiD = h5read(corr_tbl, "voice/age_rr/corRr"),
plottitle = "age - unmatched - ridge regression",
cext2 = 1.7,
mylim = mylim)
dev.off()
f <- synapser::File(title, parent=FIGURE_OUTPUT_SYN_ID)
f$annotations <- ANNOTATIONS
synStore(f, activity = Activity(
"generate confounder figure",
executed = GIT_URL,
used = c(CORR_TBL_SYN_ID, DCORR_TBL_SYN_ID)))
unlink(title)
## umatched gender ##
title <- paste0("mPower_",
gsub(" ", "_", get("metadata")$user_group),
"_supplementary_figure_18",".png")
png(title, width = 2100, height = 1300, res = 200)
GeneratePatternFigure(tapD = h5read(corr_tbl, "tap/gender_rr/corRr"),
walD = h5read(corr_tbl, "walk/gender_rr/corRr"),
resD = h5read(corr_tbl, "rest/gender_rr/corRr"),
voiD = h5read(corr_tbl, "voice/gender_rr/corRr"),
plottitle = "gender - unmatched - ridge regression",
cext2 = 1.7,
mylim = mylim)
dev.off()
f <- synapser::File(title, parent=FIGURE_OUTPUT_SYN_ID)
f$annotations <- ANNOTATIONS
synStore(f, activity = Activity(
"generate confounder figure",
executed = GIT_URL,
used = c(CORR_TBL_SYN_ID, DCORR_TBL_SYN_ID)))
unlink(title)
## umatched education ##
title <- paste0("mPower_",
gsub(" ", "_", get("metadata")$user_group),
"_supplementary_figure_19",".png")
png(title, width = 2100, height = 1300, res = 200)
GeneratePatternFigure(tapD = h5read(corr_tbl, "tap/education_rr/corRr"),
walD = h5read(corr_tbl, "walk/education_rr/corRr"),
resD = h5read(corr_tbl, "rest/education_rr/corRr"),
voiD = h5read(corr_tbl, "voice/education_rr/corRr"),
plottitle = "education - unmatched - ridge regression",
cext2 = 1.7,
mylim = mylim)
dev.off()
f <- synapser::File(title, parent=FIGURE_OUTPUT_SYN_ID)
f$annotations <- ANNOTATIONS
synStore(f, activity = Activity(
"generate confounder figure",
executed = GIT_URL,
used = c(CORR_TBL_SYN_ID, DCORR_TBL_SYN_ID)))
unlink(title)
## matched age ##
title <- paste0("mPower_",
gsub(" ", "_", get("metadata")$user_group),
"_supplementary_figure_20",".png")
png(title, width = 2100, height = 1300, res = 200)
GeneratePatternFigure(tapD = h5read(corr_tbl, "tap/age_rf/corRfM"),
walD = h5read(corr_tbl, "walk/age_rf/corRfM"),
resD = h5read(corr_tbl, "rest/age_rf/corRfM"),
voiD = h5read(corr_tbl, "voice/age_rf/corRfM"),
plottitle = "age - matched - random forest",
cext2 = 1.7,
mylim = mylim)
dev.off()
f <- synapser::File(title, parent=FIGURE_OUTPUT_SYN_ID)
f$annotations <- ANNOTATIONS
synStore(f, activity = Activity(
"generate confounder figure",
executed = GIT_URL,
used = c(CORR_TBL_SYN_ID, DCORR_TBL_SYN_ID)))
unlink(title)
## matched gender ##
title <- paste0("mPower_",
gsub(" ", "_", get("metadata")$user_group),
"_supplementary_figure_21",".png")
png(title, width = 2100, height = 1300, res = 200)
GeneratePatternFigure(tapD = h5read(corr_tbl, "tap/gender_rf/corRfM"),
walD = h5read(corr_tbl, "walk/gender_rf/corRfM"),
resD = h5read(corr_tbl, "rest/gender_rf/corRfM"),
voiD = h5read(corr_tbl, "voice/gender_rf/corRfM"),
plottitle = "gender - matched - random forest",
cext2 = 1.7,
mylim = mylim)
dev.off()
f <- synapser::File(title, parent=FIGURE_OUTPUT_SYN_ID)
f$annotations <- ANNOTATIONS
synStore(f, activity = Activity(
"generate demo confounding figure",
executed = GIT_URL, used = c(CORR_TBL_SYN_ID, DCORR_TBL_SYN_ID)))
unlink(title)
## matched education ##
title <- paste0("mPower_",
gsub(" ", "_", get("metadata")$user_group),
"_supplementary_figure_22",".png")
png(title, width = 2100, height = 1300, res = 200)
GeneratePatternFigure(tapD = h5read(corr_tbl, "tap/education_rf/corRfM"),
walD = h5read(corr_tbl, "walk/education_rf/corRfM"),
resD = h5read(corr_tbl, "rest/education_rf/corRfM"),
voiD = h5read(corr_tbl, "voice/education_rf/corRfM"),
plottitle = "education - matched - random forest",
cext2 = 1.7,
mylim = mylim)
dev.off()
f <- synapser::File(title, parent=FIGURE_OUTPUT_SYN_ID)
f$annotations <- ANNOTATIONS
synStore(f, activity = Activity(
"generate confounder figure",
executed = GIT_URL,
used = c(CORR_TBL_SYN_ID, DCORR_TBL_SYN_ID)))
unlink(title)
## matched age ##
title <- paste0("mPower_",
gsub(" ", "_", get("metadata")$user_group),
"_supplementary_figure_23",".png")
png(title, width = 2100, height = 1300, res = 200)
GeneratePatternFigure(tapD = h5read(corr_tbl, "tap/age_rr/corRrM"),
walD = h5read(corr_tbl, "walk/age_rr/corRrM"),
resD = h5read(corr_tbl, "rest/age_rr/corRrM"),
voiD = h5read(corr_tbl, "voice/age_rr/corRrM"),
plottitle = "age - matched - ridge regression",
cext2 = 1.7,
mylim = mylim)
dev.off()
f <- synapser::File(title, parent=FIGURE_OUTPUT_SYN_ID)
f$annotations <- ANNOTATIONS
synStore(f, activity = Activity(
"generate confounder figure",
executed = GIT_URL,
used = c(CORR_TBL_SYN_ID, DCORR_TBL_SYN_ID)))
unlink(title)
## matched gender ##
title <- paste0("mPower_",
gsub(" ", "_", get("metadata")$user_group),
"_supplementary_figure_24",".png")
png(title, width = 2100, height = 1300, res = 200)
GeneratePatternFigure(tapD = h5read(corr_tbl, "tap/gender_rr/corRrM"),
walD = h5read(corr_tbl, "walk/gender_rr/corRrM"),
resD = h5read(corr_tbl, "rest/gender_rr/corRrM"),
voiD = h5read(corr_tbl, "voice/gender_rr/corRrM"),
plottitle = "gender - matched - ridge regression",
cext2 = 1.7,
mylim = mylim)
dev.off()
f <- synapser::File(title, parent=FIGURE_OUTPUT_SYN_ID)
f$annotations <- ANNOTATIONS
synStore(f, activity = Activity(
"generate confounder figure",
executed = GIT_URL,
used = c(CORR_TBL_SYN_ID, DCORR_TBL_SYN_ID)))
unlink(title)
## matched education ##
title <- paste0("mPower_",
gsub(" ", "_", get("metadata")$user_group),
"_supplementary_figure_25",".png")
png(title, width = 2100, height = 1300, res = 200)
GeneratePatternFigure(tapD = h5read(corr_tbl, "tap/education_rr/corRrM"),
walD = h5read(corr_tbl, "walk/education_rr/corRrM"),
resD = h5read(corr_tbl, "rest/education_rr/corRrM"),
voiD = h5read(corr_tbl, "voice/education_rr/corRrM"),
plottitle = "education - matched - ridge regression",
cext2 = 1.7,
mylim = mylim)
dev.off()
f <- synapser::File(title, parent=FIGURE_OUTPUT_SYN_ID)
f$annotations <- ANNOTATIONS
synStore(f, activity = Activity(
"generate confounder figure",
executed = GIT_URL,
used = c(CORR_TBL_SYN_ID, DCORR_TBL_SYN_ID)))
unlink(title)
#################################################
## Compare correlation vs distance correlation
#################################################
title <- paste0("mPower_",
gsub(" ", "_", get("metadata")$user_group),
"_supplementary_figure_26",".png")
png(title, width = 2100, height = 1300, res = 200)
CompareCorVsdCorFigure(tapCor = h5read(corr_tbl, "tap/age_rf/corRfM"),
walCor = h5read(corr_tbl, "walk/age_rf/corRfM"),
resCor = h5read(corr_tbl, "rest/age_rf/corRfM"),
voiCor = h5read(corr_tbl, "voice/age_rf/corRfM"),
tapdCor = h5read(dcorr_tbl, "tap/age_rf/corRf"),
waldCor = h5read(dcorr_tbl, "walk/age_rf/corRf"),
resdCor = h5read(dcorr_tbl, "rest/age_rf/corRf"),
voidCor = h5read(dcorr_tbl, "voice/age_rf/corRf"),
plottitle = "age - cor. vs distance cor. tests - random forest",
cexleg = 1.2,
cext1 = 1.2,
cext2 = 1.7,
titlePos = -0.5)
dev.off()
f <- synapser::File(title, parent=FIGURE_OUTPUT_SYN_ID)
f$annotations <- ANNOTATIONS
synStore(f, activity = Activity(
"generate confounder figure",
executed = GIT_URL,
used = c(CORR_TBL_SYN_ID, DCORR_TBL_SYN_ID)))
unlink(title)
title <- paste0("mPower_",
gsub(" ", "_", get("metadata")$user_group),
"_supplementary_figure_27",".png")
png(title, width = 2100, height = 1300, res = 200)
CompareCorVsdCorFigure(tapCor = h5read(corr_tbl, "tap/gender_rf/corRfM"),
walCor = h5read(corr_tbl, "walk/gender_rf/corRfM"),
resCor = h5read(corr_tbl, "rest/gender_rf/corRfM"),
voiCor = h5read(corr_tbl, "voice/gender_rf/corRfM"),
tapdCor = h5read(dcorr_tbl, "tap/gender_rf/corRf"),
waldCor = h5read(dcorr_tbl, "walk/gender_rf/corRf"),
resdCor = h5read(dcorr_tbl, "rest/gender_rf/corRf"),
voidCor = h5read(dcorr_tbl, "voice/gender_rf/corRf"),
plottitle = "gender - cor. vs distance cor. tests - random forest",
cexleg = 1.2,
cext1 = 1.2,
cext2 = 1.7,
titlePos = -0.5)
dev.off()
f <- synapser::File(title, parent=FIGURE_OUTPUT_SYN_ID)
f$annotations <- ANNOTATIONS
synStore(f, activity = Activity(
"generate confounder figure",
executed = GIT_URL,
used = c(CORR_TBL_SYN_ID, DCORR_TBL_SYN_ID)))
unlink(title)
title <- paste0("mPower_",
gsub(" ", "_", get("metadata")$user_group),
"_supplementary_figure_28",".png")
png(title, width = 2100, height = 1300, res = 200)
CompareCorVsdCorFigure(tapCor = h5read(corr_tbl, "tap/education_rf/corRfM"),
walCor = h5read(corr_tbl, "walk/education_rf/corRfM"),
resCor = h5read(corr_tbl, "rest/education_rf/corRfM"),
voiCor = h5read(corr_tbl, "voice/education_rf/corRfM"),
tapdCor = h5read(dcorr_tbl, "tap/education_rf/corRf"),
waldCor = h5read(dcorr_tbl, "walk/education_rf/corRf"),
resdCor = h5read(dcorr_tbl, "rest/education_rf/corRf"),
voidCor = h5read(dcorr_tbl, "voice/education_rf/corRf"),
plottitle = "education - cor. vs distance cor. tests - random forest",
cexleg = 1.2,
cext1 = 1.2,
cext2 = 1.7,
titlePos = -0.5)
dev.off()
f <- synapser::File(title, parent=FIGURE_OUTPUT_SYN_ID)
f$annotations <- ANNOTATIONS
synStore(f, activity = Activity(
"generate confounder figure",
executed = GIT_URL,
used = c(CORR_TBL_SYN_ID, DCORR_TBL_SYN_ID)))
unlink(title)
title <- paste0("mPower_",
gsub(" ", "_", get("metadata")$user_group),
"_supplementary_figure_29",".png")
png(title, width = 2100, height = 1300, res = 200)
CompareCorVsdCorFigure(tapCor = h5read(corr_tbl, "tap/age_rr/corRrM"),
walCor = h5read(corr_tbl, "walk/age_rr/corRrM"),
resCor = h5read(corr_tbl, "rest/age_rr/corRrM"),
voiCor = h5read(corr_tbl, "voice/age_rr/corRrM"),
tapdCor = h5read(dcorr_tbl, "tap/age_rr/corRr"),
waldCor = h5read(dcorr_tbl, "walk/age_rr/corRr"),
resdCor = h5read(dcorr_tbl, "rest/age_rr/corRr"),
voidCor = h5read(dcorr_tbl, "voice/age_rr/corRr"),
plottitle = "age - cor. vs distance cor. tests - ridge regression",
cexleg = 1.2,
cext1 = 1.2,
cext2 = 1.7,
titlePos = -0.5)
dev.off()
f <- synapser::File(title, parent=FIGURE_OUTPUT_SYN_ID)
f$annotations <- ANNOTATIONS
synStore(f, activity = Activity(
"generate confounder figure",
executed = GIT_URL,
used = c(CORR_TBL_SYN_ID, DCORR_TBL_SYN_ID)))
unlink(title)
title <- paste0("mPower_",
gsub(" ", "_", get("metadata")$user_group),
"_supplementary_figure_30",".png")
png(title, width = 2100, height = 1300, res = 200)
CompareCorVsdCorFigure(tapCor = h5read(corr_tbl, "tap/gender_rr/corRrM"),
walCor = h5read(corr_tbl, "walk/gender_rr/corRrM"),
resCor = h5read(corr_tbl, "rest/gender_rr/corRrM"),
voiCor = h5read(corr_tbl, "voice/gender_rr/corRrM"),
tapdCor = h5read(dcorr_tbl, "tap/gender_rr/corRr"),
waldCor = h5read(dcorr_tbl, "walk/gender_rr/corRr"),
resdCor = h5read(dcorr_tbl, "rest/gender_rr/corRr"),
voidCor = h5read(dcorr_tbl, "voice/gender_rr/corRr"),
plottitle = "gender - cor. vs distance cor. tests - ridge regression",
cexleg = 1.2,
cext1 = 1.2,
cext2 = 1.7,
titlePos = -0.5)
dev.off()
f <- synapser::File(title, parent=FIGURE_OUTPUT_SYN_ID)
f$annotations <- ANNOTATIONS
synStore(f, activity = Activity(
"generate confounder figure",
executed = GIT_URL,
used = c(CORR_TBL_SYN_ID, DCORR_TBL_SYN_ID)))
unlink(title)
title <- paste0("mPower_",
gsub(" ", "_", get("metadata")$user_group),
"_supplementary_figure_31",".png")
png(title, width = 2100, height = 1300, res = 200)
CompareCorVsdCorFigure(tapCor = h5read(corr_tbl, "tap/education_rr/corRrM"),
walCor = h5read(corr_tbl, "walk/education_rr/corRrM"),
resCor = h5read(corr_tbl, "rest/education_rr/corRrM"),
voiCor = h5read(corr_tbl, "voice/education_rr/corRrM"),
tapdCor = h5read(dcorr_tbl, "tap/education_rr/corRr"),
waldCor = h5read(dcorr_tbl, "walk/education_rr/corRr"),
resdCor = h5read(dcorr_tbl, "rest/education_rr/corRr"),
voidCor = h5read(dcorr_tbl, "voice/education_rr/corRr"),
plottitle = "education - cor. vs distance cor. tests - ridge regression",
cexleg = 1.2,
cext1 = 1.2,
cext2 = 1.7,
titlePos = -0.5)
dev.off()
f <- synapser::File(title, parent=FIGURE_OUTPUT_SYN_ID)
f$annotations <- ANNOTATIONS
synStore(f, activity = Activity(
"generate confounder figure",
executed = GIT_URL,
used = c(CORR_TBL_SYN_ID, DCORR_TBL_SYN_ID)))
unlink(title)
}
tryCatch({
#' create logger for pipeline
sink('pipeline.log', append = TRUE)
cat(paste0(
"[",Sys.time(), "]", " Running ", SCRIPT_NAME), "\n\n")
sink()
#' run script
main()
#' store logger
sink('pipeline.log', append = TRUE)
cat(paste0("[",Sys.time(), "]", " Done Running ", SCRIPT_NAME), "\n\n")
sink()
}, error = function(e) {
sink("error.log")
cat(paste0("[",Sys.time(), "] ", SCRIPT_NAME, " - ", e), "\n\n")
sink()
stop("Stopped due to error - Please check error.log")
})
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