From dad8f526a21402ca7d573c1fa846bf3ec1cb67ef Mon Sep 17 00:00:00 2001
From: Tanushree Tunstall <tanu@tunstall.in>
Date: Tue, 9 Nov 2021 13:55:21 +0000
Subject: [PATCH] added TESTING_plots.R

---
 scripts/plotting/TESTING_PLOTS.R | 112 +++++++++++++++++++++++++++++++
 1 file changed, 112 insertions(+)
 create mode 100755 scripts/plotting/TESTING_PLOTS.R

diff --git a/scripts/plotting/TESTING_PLOTS.R b/scripts/plotting/TESTING_PLOTS.R
new file mode 100755
index 0000000..b761415
--- /dev/null
+++ b/scripts/plotting/TESTING_PLOTS.R
@@ -0,0 +1,112 @@
+#!/usr/bin/env Rscript
+getwd()
+setwd("~/git/LSHTM_analysis/scripts/plotting")
+getwd()
+source("Header_TT.R")
+
+drug = 'streptomycin'
+gene = 'gid'
+
+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
+bp_subcols_duet = "barplot_coloured_PS.svg"
+plot_bp_subcols_duet = paste0(plotdir, "/", bp_subcols_duet)
+
+##############################################################################
+# add frequency of positions (from lib data.table)
+
+setDT(subcols_df_ps)[, pos_count := .N, by = .(position)]
+
+
+foo = data.frame(subcols_df_ps$mutationinformation
+                 , subcols_df_ps$position
+                 , subcols_df_ps$pos_count)
+
+#snpsBYpos_df <- subcols_df_ps %>%
+#  group_by(position) %>%
+#  summarize(snpsBYpos = mean(pos_count))
+
+
+#********************
+# generate plot: PS
+# NO axis colours
+#********************
+g = ggplot(subcols_df_ps
+           , aes(x = factor(position, ordered = T)))
+g2 = g + geom_bar()
+
+g2
+
+foo = g2 + geom_text(stat='count', aes(label = ..count..))
+foo
+
+######
+bp_subcols_duet = "TEST_PS.svg"
+plot_bp_subcols_duet = paste0(plotdir, "/", bp_subcols_duet)
+print(paste0("plot name:", plot_bp_subcols_duet))
+svg(plot_bp_subcols_duet, width = 26, height = 4)
+
+g1 = ggplot(subcols_df_ps, aes(x = factor(position, ordered = T)
+                               , y = pos_count)) + 
+  geom_bar(stat = "summary"
+           , aes(fill = group), colour = "grey") +
+
+
+
+
+
+###################################
+
+g = ggplot(subcols_df_ps
+           , aes(x = factor(position, ordered = T)))
+outPlot_bp_ps = g + 
+  geom_bar(aes(fill = group), colour = "grey") +
+  scale_fill_manual( values = subcols_ps
+                     , guide = "none") +
+  theme( axis.text.x = element_text(size = my_xaxls
+                                    , angle = 90
+                                    , hjust = 1
+                                    , vjust = 0.4)
+         , axis.text.y = element_text(size = my_yaxls 
+                                      , angle = 0
+                                      , hjust = 1
+                                      , vjust = 0)
+         , axis.title.x = element_text(size = my_xaxts)
+         , axis.title.y = element_text(size = my_yaxts ) ) +
+  labs(title = ""
+       #title = my_title
+       , x = "Position"
+       , y = "Frequency")
+
+print(outPlot_bp_ps)
+#dev.off()
+
+######################################################################=
+#                             End of script
+######################################################################=
+