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added log bpxplots i.e boxplot_log.R

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Tanushree Tunstall 2020-10-30 13:23:29 +00:00
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commit d854f8f750
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#!/usr/bin/Rscript
getwd()
setwd("~/git/mosaic_2020/")
getwd()
############################################################
# TASK: boxplots at T1
# FIXME: currently not rendering, problem with NAs for stats?
############################################################
my_samples = "npa_sam_serum"
#=============
# Input
#=============
source("data_extraction_formatting.R")
# check: adult variable and age variable discrepancy!
metadata_all$mosaic[metadata_all$adult==1 & metadata_all$age<=18]
#=============
# Output:
#=============
outfile_bp = paste0("boxplots_log_", my_samples, ".pdf")
output_boxplot = paste0(outdir_plots, outfile_bp); output_boxplot
#===============================
# data assignment for plots
#================================
#-----------
# npa
#-----------
#wf_fp_npa = npa_wf[npa_wf$flustat == 1,]
lf_fp_npa = npa_lf[npa_lf$flustat == 1,]
lf_fp_npa$timepoint = paste0("t", lf_fp_npa$timepoint)
lf_fp_npa$timepoint = as.factor(lf_fp_npa$timepoint)
lf_fp_npa$obesity = as.factor(lf_fp_npa$obesity)
table(lf_fp_npa$mediator)
head(lf_fp_npa$value[lf_fp_npa$mediator == "vitd"])
lf_fp_npa = lf_fp_npa[!lf_fp_npa$mediator == "vitd",]
#-----------
# sam
#-----------
#wf_fp_sam = samm_wf[samm_wf$flustat == 1,]
lf_fp_sam = sam_lf[sam_lf$flustat == 1,]
lf_fp_sam$timepoint = paste0("t", lf_fp_sam$timepoint)
lf_fp_sam$timepoint = as.factor(lf_fp_sam$timepoint)
lf_fp_sam$obesity = as.factor(lf_fp_sam$obesity)
table(lf_fp_sam$mediator)
head(lf_fp_sam$value[lf_fp_sam$mediator == "vitd"])
lf_fp_sam = lf_fp_sam[!lf_fp_sam$mediator == "vitd",]
#-----------
# serum
#-----------
#wf_fp_serum = serum_wf[serum_wf$flustat == 1,]
lf_fp_serum = serum_lf[serum_lf$flustat == 1,]
lf_fp_serum$timepoint = paste0("t", lf_fp_serum$timepoint)
lf_fp_serum$timepoint = as.factor(lf_fp_serum$timepoint)
lf_fp_serum$obesity = as.factor(lf_fp_serum$obesity)
########################################################################
cat("Output plots will be in:", output_boxplot)
pdf(output_boxplot, width = 20, height = 15)
#=======================================================================
# NPA
#=======================================================================
if (is.factor(lf_fp_npa$timepoint) && is.factor(lf_fp_npa$timepoint)){
cat ("PASS: required groups are factors")
}
#------------------------------------
title_npa_log = "NPA (Log)"
#-----------------------------------
bxp_npa_log <- ggboxplot(lf_fp_npa, x = "timepoint", y = "value",
color = "obesity", palette = c("#00BFC4", "#F8766D")) +
facet_wrap(~mediator, nrow = 7, ncol = 5, scales = "free_y", shrink = F)+
scale_y_log10() +
theme(axis.text.x = element_text(size = 15)
, axis.text.y = element_text(size = 15
, angle = 0
, hjust = 1
, vjust = 0)
, axis.title.x = element_text(size = 15)
, axis.title.y = element_text(size = 15)
, plot.title = element_text(size = 20, hjust = 0.5)
, strip.text.x = element_text(size = 15, colour = "black")
, legend.title = element_text(color = "black", size = 20)
, legend.text = element_text(size = 15)
, legend.direction = "horizontal") +
labs(title = title_npa_log
, x = ""
, y = "Levels (Log)")
bxp_npa_log
#=======================================================================
# SAM
#=======================================================================
if (is.factor(lf_fp_sam$timepoint) && is.factor(lf_fp_sam$timepoint)){
cat ("PASS: required groups are factors")
}
#------------------------------------
title_sam_log = "SAM (Log)"
#-----------------------------------
bxp_sam_log <- ggboxplot(lf_fp_sam, x = "timepoint", y = "value",
color = "obesity", palette = c("#00BFC4", "#F8766D")) +
facet_wrap(~mediator, nrow = 7, ncol = 5, scales = "free_y", shrink = T)+
scale_y_log10() +
theme(axis.text.x = element_text(size = 15)
, axis.text.y = element_text(size = 15
, angle = 0
, hjust = 1
, vjust = 0)
, axis.title.x = element_text(size = 15)
, axis.title.y = element_text(size = 15)
, plot.title = element_text(size = 20, hjust = 0.5)
, strip.text.x = element_text(size = 15, colour = "black")
, legend.title = element_text(color = "black", size = 20)
, legend.text = element_text(size = 15)
, legend.direction = "horizontal") +
labs(title = title_sam_log
, x = ""
, y = "Levels (Log)")
bxp_sam_log
#=======================================================================
# SERUM
#=======================================================================
if (is.factor(lf_fp_serum$timepoint) && is.factor(lf_fp_serum$timepoint)){
cat ("PASS: required groups are factors")
}
table(lf_fp_serum$mediator)
#------------------------------------
title_serum_log = "SERUM (Log)"
#-----------------------------------
bxp_serum_log <- ggboxplot(lf_fp_serum, x = "timepoint", y = "value",
color = "obesity", palette = c("#00BFC4", "#F8766D")) +
facet_wrap(~mediator, nrow = 7, ncol = 5, scales = "free_y", shrink = T)+
scale_y_log10() +
theme(axis.text.x = element_text(size = 15)
, axis.text.y = element_text(size = 15
, angle = 0
, hjust = 1
, vjust = 0)
, axis.title.x = element_text(size = 15)
, axis.title.y = element_text(size = 15)
, plot.title = element_text(size = 20, hjust = 0.5)
, strip.text.x = element_text(size = 15, colour = "black")
, legend.title = element_text(color = "black", size = 20)
, legend.text = element_text(size = 15)
, legend.direction = "horizontal") +
labs(title = title_serum_log
, x = ""
, y = "Levels (Log)")
bxp_serum_log
#==========================================================================
dev.off()
############################################################################