242 lines
No EOL
7 KiB
R
Executable file
242 lines
No EOL
7 KiB
R
Executable file
#!/usr/bin/env Rscript
|
|
getwd()
|
|
setwd("~/git/LSHTM_analysis/scripts/plotting")
|
|
getwd()
|
|
source("~/git/LSHTM_analysis/scripts/Header_TT.R")
|
|
|
|
spec = matrix(c(
|
|
"drug" , "d", 1, "character",
|
|
"gene" , "g", 1, "character",
|
|
"data_file1" , "fa", 2, "character",
|
|
"data_file2" , "fb", 2, "character"
|
|
), byrow = TRUE, ncol = 4)
|
|
|
|
opt = getopt(spec)
|
|
|
|
drug = opt$drug
|
|
gene = opt$gene
|
|
infile_params = opt$data_file1
|
|
infile_metadata = opt$data_file2
|
|
|
|
if(is.null(drug)|is.null(gene)) {
|
|
stop("Missing arguments: --drug and --gene must both be specified (case-sensitive)")
|
|
}
|
|
|
|
#===========
|
|
# Input
|
|
#===========
|
|
|
|
source("get_plotting_dfs.R")
|
|
|
|
#===========
|
|
# output
|
|
#===========
|
|
# PS
|
|
corr_ps = "corr_PS.svg"
|
|
plot_corr_ps = paste0(plotdir,"/", corr_ps)
|
|
|
|
corr_ps_all = "corr_PS_all.svg"
|
|
plot_corr_ps_all = paste0(plotdir,"/", corr_ps_all)
|
|
|
|
|
|
# LIG
|
|
corr_lig = "corr_LIG.svg"
|
|
plot_corr_lig = paste0(plotdir,"/", corr_lig)
|
|
|
|
corr_lig_all = "corr_LIG_all.svg"
|
|
plot_corr_lig_all = paste0(plotdir,"/", corr_lig_all)
|
|
|
|
##############################################################################
|
|
foo = corr_ps_df3
|
|
#foo2 = corr_ps_df2
|
|
|
|
bar = corr_lig_df3
|
|
#bar2 = corr_lig_df2
|
|
|
|
#================================
|
|
# Data for Correlation plots: PS
|
|
#================================
|
|
# subset data to generate pairwise correlations
|
|
cols_to_select = c("DUET"
|
|
, "Foldx"
|
|
, "Log (OR)"
|
|
, "-Log (P)"
|
|
, "MAF"
|
|
, "duet_outcome"
|
|
, drug)
|
|
corr_data_ps = foo[names(foo)%in%cols_to_select]
|
|
length(cols_to_select)
|
|
|
|
colnames(corr_data_ps)
|
|
|
|
start = 1
|
|
end = which(colnames(corr_data_ps) == drug); end # should be the last column
|
|
offset = 1
|
|
|
|
my_corr_ps = corr_data_ps[start:(end - offset)]
|
|
head(my_corr_ps)
|
|
|
|
#---------------------
|
|
# Corr plot PS: short
|
|
# data: corr_ps_df3
|
|
# cols: 7
|
|
#---------------------
|
|
cat("Corr plot PS DUET with coloured dots:", plot_corr_ps)
|
|
svg(plot_corr_ps, width = 15, height = 15)
|
|
|
|
pairs.panels(my_corr_ps[1:(length(my_corr_ps)-1)]
|
|
, method = "spearman" # correlation method
|
|
, hist.col = "grey" ##00AFBB
|
|
, density = TRUE # show density plots
|
|
, ellipses = F # show correlation ellipses
|
|
, stars = T
|
|
, rug = F
|
|
, breaks = "Sturges"
|
|
, show.points = T
|
|
, bg = c("#f8766d", "#00bfc4")[unclass(factor(my_corr_ps$duet_outcome))] # foldx colours are reveresed
|
|
, pch = 21 # for bg
|
|
, jitter = T
|
|
, alpha = 1
|
|
, cex = 1.8
|
|
, cex.axis = 2
|
|
, cex.labels = 4
|
|
, cex.cor = 1
|
|
, smooth = F
|
|
)
|
|
dev.off()
|
|
|
|
corr_ps_rho = corr.test(my_corr_ps[1:5], method = "spearman")$r
|
|
corr_ps_p = corr.test(my_corr_ps[1:5], method = "spearman")$p
|
|
|
|
#---------------------
|
|
# Corr plot PS: ALL
|
|
# data: corr_ps_df3
|
|
# cols: 10
|
|
#---------------------
|
|
end_ps_all = which(colnames(foo) == drug); end_ps_all # should be the last column
|
|
|
|
my_corr_ps_all = foo[start:(end_ps_all - offset)]
|
|
cols_to_drop = "Mutation"
|
|
my_corr_ps_all = my_corr_ps_all[, !(names(my_corr_ps_all)%in%cols_to_drop)]
|
|
head(my_corr_ps_all)
|
|
length(colnames(my_corr_ps_all))
|
|
|
|
cat("Corr plot PS DUET with coloured dots:", plot_corr_ps_all)
|
|
svg(plot_corr_ps_all, width = 15, height = 15)
|
|
|
|
pairs.panels(my_corr_ps_all[1:(length(my_corr_ps_all)-1)]
|
|
, method = "spearman" # correlation method
|
|
, hist.col = "grey" ##00AFBB
|
|
, density = TRUE # show density plots
|
|
, ellipses = F # show correlation ellipses
|
|
, stars = T
|
|
, rug = F
|
|
, breaks = "Sturges"
|
|
, show.points = T
|
|
, bg = c("#f8766d", "#00bfc4")[unclass(factor(my_corr_ps_all$duet_outcome))] # foldx colours are reveresed
|
|
, pch = 21 # for bg
|
|
, jitter = T
|
|
, alpha = 1
|
|
, cex = 1.5
|
|
, cex.axis = 2
|
|
, cex.labels = 2.5
|
|
, cex.cor = 1
|
|
, smooth = F
|
|
)
|
|
dev.off()
|
|
|
|
#==================================
|
|
# Data for Correlation plots: LIG
|
|
#==================================
|
|
cols_to_select_lig = c("Ligand Affinity"
|
|
, "Log (OR)"
|
|
, "-Log (P)"
|
|
, "MAF"
|
|
, "ligand_outcome"
|
|
, drug)
|
|
|
|
corr_data_lig = bar[names(bar)%in%cols_to_select_lig]
|
|
length(cols_to_select_lig)
|
|
|
|
colnames(corr_data_lig)
|
|
|
|
start_lig = 1
|
|
end_lig = which(colnames(corr_data_lig) == drug); end_lig # should be the last column
|
|
offset_lig = 1
|
|
|
|
my_corr_lig = corr_data_lig[start_lig:(end_lig-offset_lig)]
|
|
head(my_corr_lig)
|
|
|
|
#---------------------
|
|
# Corr plot LIG: short
|
|
# data: corr_lig_df3
|
|
# cols: 7
|
|
#---------------------
|
|
cat("Corr LIG plot with coloured dots:", plot_corr_lig)
|
|
svg(plot_corr_lig, width = 15, height = 15)
|
|
|
|
pairs.panels(my_corr_lig[1:(length(my_corr_lig)-1)]
|
|
, method = "spearman" # correlation method
|
|
, hist.col = "grey" ##00AFBB
|
|
, density = TRUE # show density plots
|
|
, ellipses = F # show correlation ellipses
|
|
, stars = T
|
|
, rug = F
|
|
, breaks = "Sturges"
|
|
, show.points = T
|
|
, bg = c("#f8766d", "#00bfc4")[unclass(factor(my_corr_lig$ligand_outcome))]
|
|
, pch = 21 # for bg
|
|
, jitter = T
|
|
, cex = 2
|
|
, cex.axis = 2
|
|
, cex.labels = 4
|
|
, cex.cor = 1
|
|
, smooth = F
|
|
)
|
|
|
|
dev.off()
|
|
|
|
corr_lig_rho = corr.test(my_corr_lig[1:4], method = "spearman")$r
|
|
corr_lig_p = corr.test(my_corr_lig[1:4], method = "spearman")$p
|
|
|
|
#---------------------
|
|
# Corr plot LIG: ALL
|
|
# data: corr_lig_df3
|
|
# cols: 9
|
|
#---------------------
|
|
end_lig_all = which(colnames(bar) == drug); end_lig_all # should be the last column
|
|
|
|
my_corr_lig_all = bar[start_lig:(end_lig_all - offset_lig)]
|
|
cols_to_drop = "Mutation"
|
|
my_corr_lig_all = my_corr_lig_all[, !(names(my_corr_lig_all)%in%cols_to_drop)]
|
|
head(my_corr_lig_all)
|
|
length(colnames(my_corr_lig_all))
|
|
|
|
cat("Corr plot LIG with coloured dots:", plot_corr_lig_all)
|
|
svg(plot_corr_lig_all, width = 15, height = 15)
|
|
|
|
pairs.panels(my_corr_lig_all[1:(length(my_corr_lig_all)-1)]
|
|
, method = "spearman" # correlation method
|
|
, hist.col = "grey" ##00AFBB
|
|
, density = TRUE # show density plots
|
|
, ellipses = F # show correlation ellipses
|
|
, stars = T
|
|
, rug = F
|
|
, breaks = "Sturges"
|
|
, show.points = T
|
|
, bg = c("#f8766d", "#00bfc4")[unclass(factor(my_corr_lig_all$ligand_outcome))] # foldx colours are reveresed
|
|
, pch = 21 # for bg
|
|
, jitter = T
|
|
, alpha = 1
|
|
, cex = 1.5
|
|
, cex.axis = 2
|
|
, cex.labels = 2.2
|
|
, cex.cor = 1
|
|
, smooth = F
|
|
)
|
|
dev.off()
|
|
|
|
|
|
######################################################################=
|
|
# End of script
|
|
######################################################################= |