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added boxplot_stat.R to output plots for all sample types

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Tanushree Tunstall 2020-11-01 16:46:42 +00:00
parent dc775a4486
commit 4ca975bf81
1 changed files with 71 additions and 0 deletions
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#!/usr/bin/Rscript
getwd()
setwd("~/git/mosaic_2020/")
getwd()
###############################################################
source("boxplot_stat_function.R")
source("plot_data.R")
#=============
# Output:
#=============
outfile_bp = paste0("boxplots_stats_all", ".pdf")
output_boxplot_stats = paste0(outdir_plots, outfile_bp); output_boxplot_stats
pdf(output_boxplot_stats, width=22, height=16)
#===========================
# NPA
#===========================
my_sample_npa = "NPA"
plots_npa = doMyPlots(lf_fp_npa)
npa_plot = ggpubr::ggarrange(plotlist = plots_npa
, align = "hv"
, ncol = 7
, nrow = 5
, common.legend = T)
#npa_plot
npa_plot_annot = annotate_figure(npa_plot
, top = text_grob(my_sample_npa, color = "blue", face = "bold", size = 14)
, bottom = text_grob("Mosaic data\nFlu positive adults (n=133)"
, color = "blue"
, hjust = 1, x = 0.98, face = "italic", size = 10)
, left = text_grob("Levels (pg/ml)", color = "black", rot = 90, size = 18))
npa_plot_annot
#dev.off()
#===========================
# SAM
#===========================
my_sample_sam = "SAM"
plots_sam = doMyPlots(lf_fp_sam)
sam_plot = ggpubr::ggarrange(plotlist = plots_sam
, align = "hv"
, ncol = 7
, nrow = 5
, common.legend = T)
#sam_plot
sam_plot_annot = annotate_figure(sam_plot
, top = text_grob(my_sample_sam, color = "blue", face = "bold", size = 14)
, bottom = text_grob("Mosaic data\nFlu positive adults (n=133)"
, color = "blue"
, hjust = 1, x = 0.98, face = "italic", size = 10)
, left = text_grob("Levels (pg/ml)", color = "black", rot = 90, size = 18))
sam_plot_annot
#dev.off()
#===========================
# SERUM
#===========================
my_sample_serum = "serum"
plots_serum = doMyPlots(lf_fp_serum)
serum_plot = ggpubr::ggarrange(plotlist = plots_serum
, align = "hv"
, ncol = 7
, nrow = 5
, common.legend = T)
#serum_plot
serum_plot_annot = annotate_figure(serum_plot
, top = text_grob(my_sample_serum, color = "blue", face = "bold", size = 14)
, bottom = text_grob("Mosaic data\nFlu positive adults (n=133)"
, color = "blue"
, hjust = 1, x = 0.98, face = "italic", size = 10)
, left = text_grob("Levels (pg/ml)", color = "black", rot = 90, size = 18))
serum_plot_annot
dev.off()