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This commit is contained in:
Tanushree Tunstall 2020-11-02 12:05:55 +00:00
parent ee35e1cb20
commit 9fc9a5852b
5 changed files with 96 additions and 40 deletions
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11
plot_data.R Normal file → Executable file
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@ -6,7 +6,7 @@ getwd()
# TASK: boxplots at T1
# FIXME: currently not rendering, problem with NAs for stats?
############################################################
my_samples = "npa_sam_serum"
#=============
# Input
#=============
@ -15,12 +15,6 @@ source("data_extraction_formatting.R")
# check: adult variable and age variable discrepancy!
metadata_all$mosaic[metadata_all$adult==1 & metadata_all$age<=18]
#=============
# Output:
#=============
outfile_bp = paste0("boxplots_linear_", my_samples, ".pdf")
output_boxplot = paste0(outdir_plots, outfile_bp); output_boxplot
#===============================
# data assignment for plots
#================================
@ -36,6 +30,7 @@ lf_fp_npa$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$mediator == "vitd",]
table(lf_fp_npa$mediator)
#-----------
# sam
@ -49,6 +44,7 @@ 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",]
table(lf_fp_sam$mediator)
#-----------
# serum
@ -59,4 +55,5 @@ lf_fp_serum$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$obesity)
head(lf_fp_sam$value[lf_fp_serum$mediator == "vitd"])
########################################################################