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_plot.R

@@ -1,106 +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_or_plotname = "logo_or_plot.svg"
-plot_logo_or = paste0(plotdir,"/", logo_or_plotname)
-
-logo_logOR_plotname = "logo_logOR_plot.svg"
-plot_logo_logOR = paste0(plotdir,"/", logo_logOR_plotname)
-
-##############################################################################
-
-#================================
-# Logo plot: custom height (OR)   
-#================================ 
-cat("Logo plot with OR as y axis:", plot_logo_or)
-svg(plot_logo_or, width = 30 , height = 6)
-
-logo_or = ggseqlogo(wide_df_or
-                    , method = "custom"
-                    , seq_type = "aa") + ylab("my custom height") +
-    theme( axis.text.x = element_text(size = 12
-                                       , angle = 90
-                                       , hjust = 1
-                                       , vjust = 0.4)
-          , axis.text.y = element_text(size = 22
-                                       , angle = 0
-                                       , hjust = 1
-                                       , vjust = 0)
-          , axis.title.y = element_text(size = 25)
-          , axis.title.x = element_text(size = 20)
-          #, legend.position = "bottom") + 
-          , legend.position = "none")+
-          #, legend.text = element_text(size = 15)
-          #, legend.title = element_text(size = 15))+
-      scale_x_discrete("Position"
-                     #, breaks
-                     , labels = position_or
-                     , limits = factor(1:length(position_or))) +
-  ylab("Odds Ratio")
-  
-print(logo_or)
-dev.off()
-
-#=======================================
-# Logo plot: custom height (Log10 OR) 
-#=======================================
-cat("Logo plot with log10 OR as y axis:", plot_logo_logOR)
-svg(plot_logo_logOR, width = 30 , height = 6)
-
-logo_logOR = ggseqlogo(wide_df_logor_m
-          , method = "custom"
-          , seq_type="aa") + ylab("my custom height") +
-  theme(legend.position = "bottom"
-        , axis.text.x = element_text(size = 13
-                                     , angle = 90
-                                     , hjust = 1
-                                     , vjust = 0.4)
-        , axis.text.y = element_text(size = 20
-                                     , angle = 0
-                                     , hjust = 1
-                                     , vjust = 0)
-        , axis.title.y = element_text(size = 25)
-        , axis.title.x = element_text(size = 20))+
-  scale_x_discrete("Position"
-                   #, breaks
-                   , labels = position_logor
-                   , limits = factor(1:length(position_logor)))+
-  ylab("Log (Odds Ratio)") + 
-  scale_y_continuous(limits = c(0, 9))
-
-print(logo_logOR)
-dev.off()
-
-######################################################################=
-#                             End of script
-######################################################################=