diff --git a/plot_data.R b/plot_data.R new file mode 100644 index 0000000..4df2c41 --- /dev/null +++ b/plot_data.R @@ -0,0 +1,62 @@ +#!/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$age<=18] + +#============= +# Output: +#============= +outfile_bp = paste0("boxplots_linear_", my_samples, ".pdf") +output_boxplot = paste0(outdir_plots, outfile_bp); output_boxplot + +#=============================== +# data assignment for plots +#================================ +#----------- +# npa +#----------- +#wf_fp_npa = npa_wf[npa_wf$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) + +######################################################################## \ No newline at end of file