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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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110
boxplot_stat_all.R Normal file → Executable file
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@ -3,19 +3,31 @@ getwd()
setwd("~/git/mosaic_2020/")
getwd()
###############################################################
#=============
# Input
#=============
source("boxplot_stat_function.R")
source("plot_data.R")
#=============
# Output:
# 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$mosaic)); fp_npa
cat("\nPlotting boxplots with stats for:", my_sample_npa
, "\n========================================================\n")
plots_npa = doMyPlots(lf_fp_npa)
npa_plot = ggpubr::ggarrange(plotlist = plots_npa
, align = "hv"
@ -24,36 +36,64 @@ npa_plot = ggpubr::ggarrange(plotlist = plots_npa
, common.legend = T)
#npa_plot
npa_plot_annot = annotate_figure(npa_plot
, top = text_grob(my_sample_npa, color = "blue", face = "bold", size = 14)
, bottom = text_grob("Mosaic data\nFlu positive adults (n=133)"
, top = text_grob(my_sample_npa
, color = "blue"
, face = "bold"
, size = 14)
, bottom = text_grob(paste0("Mosaic data\nFlu positive adults (n=", fp_npa, ")")
, color = "blue"
, hjust = 1, x = 0.98, face = "italic", size = 10)
, left = text_grob("Levels (pg/ml)", color = "black", rot = 90, size = 18))
, hjust = 1
, x = 0.98
, face = "italic"
, size = 10)
, left = text_grob("Levels (pg/ml)"
, color = "black"
, rot = 90
, size = 18))
npa_plot_annot
#dev.off()
#===========================
#-------------
# SAM
#===========================
my_sample_sam = "SAM"
plots_sam = doMyPlots(lf_fp_sam)
sam_plot = ggpubr::ggarrange(plotlist = plots_sam
, align = "hv"
, ncol = 7
, nrow = 5
, common.legend = T)
#-------------
#my_sample_sam = "SAM"
#fp_sam = length(unique(lf_fp_sam$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("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
#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 = doMyPlots(lf_fp_serum)
serum_plot = ggpubr::ggarrange(plotlist = plots_serum
, align = "hv"
@ -62,10 +102,20 @@ serum_plot = ggpubr::ggarrange(plotlist = plots_serum
, 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)"
, 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))
, 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()
###############################################################