moved old logo plots scripts to redundant and updated running_plotting_scripts.txt to reflect these and how to run the single logo_plots.R to generate logo plots

scripts/plotting/logo_multiple_muts.R

@@ -1,118 +0,0 @@
-#!/usr/bin/env Rscript
-getwd()
-setwd("~/git/LSHTM_analysis/scripts/plotting")
-getwd()
-source("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
-#===========
-logo_multiple_muts = "logo_multiple_muts.svg"
-plot_logo_multiple_muts = paste0(plotdir,"/", logo_multiple_muts)
-
-#*********************
-# Plot 1: mutant logo
-#*********************
-p0 = ggseqlogo(tab_mt
-               , method = 'custom'
-               , seq_type = 'aa') + 
-  #ylab('my custom height') +
-  theme(axis.text.x = element_blank()) +
-  theme(text=element_text(family="FreeSans"))+
-  theme_logo()+ 
-  scale_x_continuous(breaks = 1:ncol(tab_mt)
-                     , labels = colnames(tab_mt))+
-  scale_y_continuous( breaks = 1:max_mult_mut
-                      , limits = c(0, max_mult_mut))
-
-p0
-cat('\nDone: p0')
-
-# further customisation
-mut_logo_p = p0 + theme(legend.position = "none"
-                        , legend.title = element_blank()
-                        , legend.text = element_text(size = 20)
-                        , axis.text.x = element_text(size = 17, angle = 90)
-                        , axis.text.y = element_blank())
-#mut_logo_p
-cat('\nDone: p0+mut_logo_p')
-
-#***********************
-# Plot 2: wild_type logo
-#***********************
-p2 = ggseqlogo(tab_wt
-               , method = 'custom'
-               , seq_type = 'aa'
-               #, col_scheme = "taylor"
-               #, col_scheme = chemistry2
-) + 
-  #ylab('my custom height') +
-  theme(text=element_text(family="FreeSans"))+
-  theme(axis.text.x = element_blank()
-        , axis.text.y = element_blank()) +
-  theme_logo() +
-  scale_x_continuous(breaks = 1:ncol(tab_wt)
-                     , labels = colnames(tab_wt)) 
-#p2
-cat('\nDone: p2 done')
-
-# further customise
-wt_logo_p = p2 +
-  theme(legend.position = "bottom"
-        #, legend.title = element_blank()
-        , legend.title = element_text("Amino acid properties", size = 20)
-        , legend.text = element_text(size = 20)
-        , axis.text.x = element_text(size = 17, angle = 90)
-        , axis.text.y = element_blank()
-        , axis.title.x = element_text(size = 22))+
-  
-  labs(x= "Position")
-
-#wt_logo_p
-cat('\nDone: wt_logo_p')
-
-#------------------------------------
-# Now combine using cowplot
-# which ensures the plots are aligned
-#------------------------------------
-#suppressMessages( require(cowplot) )
-cat('\nDone: wt_logo_p')
-
-#plot_grid(p1, p3, ncol = 1, align = 'v') 
-cat('\nDone: mut_logo_p + wt_logo_p')
-
-# colour scheme: https://rdrr.io/cran/ggseqlogo/src/R/col_schemes.r
-cat("\nOutput plot:", plot_logo_multiple_muts, "\n")
-svg(plot_logo_multiple_muts, width = 32, height = 10)
-
-mult_muts_combined = cowplot::plot_grid(mut_logo_p, wt_logo_p
-                                        , nrow = 2
-                                        , align = "v"
-                                        , rel_heights = c(3/4, 1/4))
-
-print(mult_muts_combined)
-#dev.off()