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added boxplot_stat_log.R to generate graphs with log data and stats

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Tanushree Tunstall 2020-11-02 14:28:52 +00:00
parent 550e8b2c50
commit b8ff7995ac
6 changed files with 249 additions and 10 deletions
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boxplot_stat_log.R Normal file
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#!/usr/bin/Rscript
getwd()
setwd("~/git/mosaic_2020/")
getwd()
###############################################################
#=============
# Input
#=============
source("boxplot_stat_function.R")
source("plot_data.R")
#=============
# Output
#=============
outfile_bp = paste0("boxplots_stats_npa_serum_LOG", ".pdf")
output_boxplot_stats = paste0(outdir_plots, outfile_bp); output_boxplot_stats
pdf(output_boxplot_stats, width=22, height=16)
###############################################################
#===============================
# data assignment for plots
#===============================
#----------------------------------------
#-------
# NPA
#-------
# vl data juggling with 0!
vl_temp_fix = lf_fp_npa[lf_fp_npa$mediator=="vl_pfu_ul",]
vl_temp_fix$value[1:20]
vl_temp_fix$value[vl_temp_fix$value == 0] <- 1
vl_temp_fix$value[1:20]
orig_nrow = nrow(lf_fp_npa); orig_nrow; table(lf_fp_npa$mediator)
lf_fp_npa = lf_fp_npa[!lf_fp_npa$mediator=="vl_pfu_ul",]
temp_nrow = nrow(lf_fp_npa); temp_nrow; table(lf_fp_npa$mediator)
# add vl_temp_fix back
lf_fp_npa = rbind(lf_fp_npa, vl_temp_fix)
revised_nrow = nrow(lf_fp_npa); revised_nrow
orig_nrow == revised_nrow
head(lf_fp_npa$value)
# log all values and reassign
lf_fp_npa$value = log10(lf_fp_npa$value)
head(lf_fp_npa$value)
vl_temp_fix2 = lf_fp_npa[lf_fp_npa$mediator=="vl_pfu_ul",]
vl_temp_fix2$value[1:20]
#------------------------------------------
my_sample_npa = "NPA"
fp_npa = length(unique(lf_fp_npa$mosaic)); fp_npa
cat("\nPlotting boxplots with stats for:", my_sample_npa
, "\n========================================================\n")
plots_npa = doMyPlotsStats(lf_fp_npa)
npa_plot = ggpubr::ggarrange(plotlist = plots_npa
, align = "hv"
, ncol = 7
, nrow = 5
, common.legend = T)
#npa_plot
npa_plot_annot = annotate_figure(npa_plot
, top = text_grob(my_sample_npa
, color = "blue"
, face = "bold"
, size = 14)
, bottom = text_grob(paste0("Mosaic data\nFlu positive adults (n=", fp_npa, ")")
, color = "blue"
, hjust = 1
, x = 0.98
, face = "italic"
, size = 10)
, left = text_grob("Levels (pg/ml)"
, color = "black"
, rot = 90
, size = 18))
npa_plot_annot
#dev.off()
#-------------
# SAM
#-------------
#my_sample_sam = "SAM"
#fp_sam = length(unique(lf_fp_sam$mosaic)); fp_sam
#cat("\nPlotting boxplots with stats for:", my_sample_sam
# , "\n========================================================\n")
#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(paste0("Mosaic data\nFlu positive adults (n=", fp_sam, ")")
# , 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
#-------------
head(lf_fp_serum$value)
# reassign
lf_fp_serum$value = log10(lf_fp_serum$value)
head(lf_fp_serum$value)
my_sample_serum = "serum"
fp_serum = length(unique(lf_fp_serum$mosaic)); fp_serum
cat("\nPlotting boxplots with stats for:", my_sample_serum
, "\n========================================================\n")
plots_serum = doMyPlotsStats(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(paste0("Mosaic data\nFlu positive adults (n=", fp_serum, ")")
, 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()
###############################################################