replaced old lineage barplot with count and diversity combined plots sourced from function

scripts/plotting/lineage_basic_barplots_combined.R

@@ -0,0 +1,128 @@
+#!/usr/bin/env Rscript       
+getwd()
+setwd("~/git/LSHTM_analysis/scripts/plotting/")
+getwd()
+#########################################################
+# TASK: Basic lineage barplot showing numbers
+
+# Output: Basic barplot with lineage samples and mut count
+
+##########################################################
+# 				Installing and loading required packages 			 
+##########################################################
+source("Header_TT.R")
+source("../functions/bp_lineage.R")
+
+#===========
+# input
+#===========
+source ('get_plotting_dfs.R')
+
+cat("Directories imported:"
+    , "\n===================="
+    , "\ndatadir:", datadir
+    , "\nindir:", indir
+    , "\noutdir:", outdir
+    , "\nplotdir:", plotdir)
+
+cat("Variables imported:"
+    , "\n====================="
+    , "\ndrug:", drug
+    , "\ngene:", gene
+    , "\ngene_match:", gene_match
+    , "\nAngstrom symbol:", angstroms_symbol
+    #, "\nNo. of duplicated muts:", dup_muts_nu
+    , "\ndr_muts_col:", dr_muts_col
+    , "\nother_muts_col:", other_muts_col
+    , "\ndrtype_col:", resistance_col)
+
+#=======
+# output
+#=======
+# plot 1
+basic_bp_lineage_cl = "basic_lineage_barplots_combined.svg"
+plot_basic_bp_lineage_cl  =  paste0(plotdir,"/", basic_bp_lineage_cl)
+plot_basic_bp_lineage_cl 
+#################################################################
+#=============================
+# PLOT 1: Lineage count plot:
+# LF data
+#=============================
+#------------------------
+# Data: All lineages or
+# selected few
+#------------------------
+sel_lineages = levels(lin_lf$sel_lineages_f)[1:4]
+sel_lineages
+lin_lf_plot = lin_lf[lin_lf$sel_lineages_f%in%sel_lineages,]
+str(lin_lf_plot)
+
+# drop unused factor levels
+lin_lf_plot$sel_lineages_f = factor(lin_lf_plot$sel_lineages_f)
+levels(lin_lf_plot$sel_lineages_f)
+str(lin_lf_plot)
+
+#------------------------
+# plot from my function:
+#------------------------
+lin_countP = lin_count_bp(lin_lf_plot
+             , x_categ = "sel_lineages_f"
+             , y_count = "p_count"
+             , bar_fill_categ = "count_categ"
+             , display_label_col = "p_count"
+             , bar_stat_stype = "identity"
+             , x_lab_angle = 90
+             , my_xats = 20
+             , bar_col_labels = c("Mutations", "Total Samples")
+             , bar_col_values = c("grey50", "gray75")
+             , y_scale_percent = F # T for diversity
+             , y_log10 = F
+             , y_label = "Count")
+lin_countP
+#================================
+# PLOT 2: Lineage Diversity plot
+# WF data
+#================================
+#------------------------
+# Data: All lineages or
+# selected few
+#------------------------
+sel_lineages = levels(lin_wf$sel_lineages_f)[1:4]
+sel_lineages
+lin_wf_plot = lin_wf[lin_wf$sel_lineages_f%in%sel_lineages,]
+str(lin_wf_plot)
+
+# drop unused factor levels
+lin_wf_plot$sel_lineages_f = factor(lin_wf_plot$sel_lineages_f)
+levels(lin_wf_plot$sel_lineages_f)
+str(lin_wf_plot)
+
+#------------------------
+# plot from my function:
+#------------------------
+lin_diversityP = lin_count_bp(lin_wf_plot
+             , x_categ = "sel_lineages_f"
+             , y_count = "snp_diversity"
+             , display_label_col = "snp_diversity_f"
+             , bar_stat_stype = "identity"
+             , x_lab_angle = 90
+             , my_xats = 20
+             , y_scale_percent = T
+             , y_label = "SNP diversity")
+
+lin_diversityP
+#########################################################################333
+#================================
+# Combine plots
+#================================
+
+svg(plot_basic_bp_lineage_cl , width = 8, height = 15 )
+
+lineage_bp_combined = cowplot::plot_grid(lin_countP, lin_diversityP
+                                      #, labels = c("(a)", "(b)", "(c)", "(d)")
+                                      , nrow = 2
+                                      , labels = "AUTO"
+                                      , label_size = 25)
+
+lineage_bp_combined
+dev.off()