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mosaic_2020/boxplots_stat_ob_paper.R

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#!/usr/bin/Rscript
getwd()
setwd("~/git/mosaic_2020/")
getwd()
###############################################################
# TASK: boxplots with stats for NPA, SAM and SERUM
# for each mediator, at each timepoint by group
# TODO: check boxplot_stat_function.R
# output plots even if stats fail due to data containing only LLODs
# however for a given mediator, if there is error for ANY timepoint
# stats will not be added for the entire plot! To be handled in
# next iteration!
###############################################################
#=============
# Input
#=============
source("boxplot_stat_function.R")
source("plot_data_ob_paper.R")
#=============
# Output
#=============
outdir_plots_paper = "/home/tanu/git/mosaic_2020/output/plots_paper/"
#outfile_bp = paste0("boxplots_stats_paper-%03d.png")
#output_boxplot_stats = paste0(outdir_plots_paper, outfile_bp); output_boxplot_stats
#svg(output_boxplot_stats, width=22, height=16)
#png(output_boxplot_stats, width = 11, height = 8, units = "in", res = 300)
###############################################################
#===============================
# data assignment for plots
#===============================
#-------------
# NPA: VL
#-------------
#linear
cat("plotting for FP adult patients:",
length(unique(vl_lf_plot_df$mosaic)))
# linear : but data is not visible
plots_npa_vl = doMyPlotsStats(vl_lf_plot_df)
npa_plot_vl = ggpubr::ggarrange(plotlist = plots_npa_vl
, align = "hv"
#, legend = c(0.8,1)
#, legend = "bottom"
, common.legend = T)
npa_plot_vl
# log
plots_npa_vl_log = doMyPlotsStats(vl_lf_plot_df_log)
npa_plot_vl_log = ggpubr::ggarrange(plotlist = plots_npa_vl_log
, align = "hv"
, common.legend = T
)
npa_plot_vl_log
############################################################
mediator_order = c("IFN-α2a","IFN-β", "IFN-γ", "IL-1", "IL-6", "CXCL8", "CXCL10", "TNF-α")
#-----------------------------
# NPA: selected mediators
#-----------------------------
# linear
plots_npa = doMyPlotsStats(npa_lf_plot_df, custom_order = mediator_order)
npa_plot_1 = ggpubr::ggarrange(plotlist = plots_npa
, align = "hv"
, ncol = 8
, nrow = 1
, common.legend = T)
npa_plot = annotate_figure(npa_plot_1,
top = text_grob("NPA"
, color = "black"
#, face = "bold"
, size = 14))
# log
plots_npa_log = doMyPlotsStats(npa_lf_plot_df_log, custom_order = mediator_order)
npa_plot_log_1 = ggpubr::ggarrange(plotlist = plots_npa_log
, align = "hv"
, ncol = 8
, nrow = 1
, common.legend = T)
npa_plot_log = annotate_figure(npa_plot_log_1,
top = text_grob("NPA"
, color = "black"
#, face = "bold"
, size = 14))
npa_plot_log
#-------------------------------
# SERUM: selected mediators
#--------------------------------
# linear
plots_serum = doMyPlotsStats(serum_lf_plot_df, custom_order = mediator_order)
serum_plot_1 = ggpubr::ggarrange(plotlist = plots_serum
, align = "hv"
, ncol = 8
, nrow = 1
, common.legend = F
)
serum_plot = annotate_figure(serum_plot_1,
top = text_grob("Serum"
, color = "black"
#, face = "bold"
, size = 14))
serum_plot
# log
plots_serum_log = doMyPlotsStats(serum_lf_plot_log, custom_order = mediator_order)
serum_plot_log_1 = ggpubr::ggarrange(plotlist = plots_serum_log
, align = "hv"
, ncol = 8
, nrow = 1
, common.legend = F)
serum_plot_log = annotate_figure(serum_plot_log_1,
top = text_grob("Serum"
, color = "black"
#, face = "bold"
, size = 14))
serum_plot_log
##############################################################
##############################################################
cat ("Outplots will be in:", outdir_plots_paper)
#======================
# Output: Linear graphs
#======================
# viral load: linear
viral_load_annot = annotate_figure(
npa_plot_vl
, left = text_grob("pg/ml"
, color = "black"
, rot = 90
, size = 18)
)
png(paste0(outdir_plots_paper, "viral_load_linear"),
width = 5,
height = 5,
units = "in",
res = 300)
viral_load_annot
dev.off()
# npa and serum mediators: linear
outplot_linear = cowplot::plot_grid(
npa_plot,
serum_plot,
nrow = 2,
rel_heights = c(1.15,1)
)
outplot_linear_annot = annotate_figure(
outplot_linear
, left = text_grob("pg/ml"
, color = "black"
, rot = 90
, size = 16)
)
png(paste0(outdir_plots_paper, "npa_serum_linear"),
width = 18,
height = 6,
units = "in",
res = 300)
outplot_linear_annot
dev.off()
#======================
# Output: Log graphs
#======================
# viral load: log
viral_load_log_annot = annotate_figure(
npa_plot_vl_log
, left = text_grob("Log10 (pg/ml)"
, color = "black"
, rot = 90
, size = 18)
)
png(paste0(outdir_plots_paper, "viral_load_log" ),
width = 5,
height = 5,
units = "in",
res = 300)
viral_load_log_annot
dev.off()
# npa and serum mediators: log
outplot_log = cowplot::plot_grid(
npa_plot_log,
serum_plot_log,
nrow = 2,
rel_heights = c(1.15,1)
)
outplot_log_annot = annotate_figure(
outplot_log
, left = text_grob("Log10 (pg/ml)"
, color = "black"
, rot = 90
, size = 16)
)
png(paste0(outdir_plots_paper, "npa_serum_log"),
width = 18,
height = 6,
units = "in",
res = 300)
outplot_log_annot
dev.off()
###############################################################
# END OF SCRIPT #
###############################################################
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