121 lines
5.1 KiB
R
Executable file
121 lines
5.1 KiB
R
Executable file
#!/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_all", ".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
|
|
#-------------
|
|
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
|
|
#-------------
|
|
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()
|
|
###############################################################
|