added boxplots_stat_ob_paper.R and plot_data_ob_paper.R
This commit is contained in:
parent
dc7e277a72
commit
7011dc75fa
2 changed files with 447 additions and 0 deletions
225
boxplots_stat_ob_paper.R
Normal file
225
boxplots_stat_ob_paper.R
Normal file
|
|
@ -0,0 +1,225 @@
|
|||
#!/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 #
|
||||
###############################################################
|
||||
Loading…
Add table
Add a link
Reference in a new issue