saving work

scripts/plotting/plotting_thesis/alr/gg_pairs_all_alr.R

@@ -5,7 +5,7 @@
 #=======
 # output
 #=======
-outdir_images = paste0("/home/pub/Work/LSHTM/Thesis_Plots/pairs/")
+#outdir_images = paste0("/home/pub/Work/LSHTM/Thesis_Plots/pairs/")
 #cat("plots will output to:", outdir_images)
 
 custom_cor <- function(data, mapping, method, ...){
@@ -80,7 +80,7 @@ corr_plotdf = corr_data_extract(merged_df3
 
 aff_dist_cols = colnames(corr_plotdf)[grep("Dist", colnames(corr_plotdf))]
 static_cols =  c("Log10(MAF)"
-                 , "Log10(OR)"
+                 #, "Log10(OR)"
 )
 ############################################################
 #=============================================

scripts/plotting/plotting_thesis/linage_bp_dist.R

@@ -1,165 +0,0 @@
-#!/usr/bin/env Rscript  
-
-#########################################################
-# TASK: Lineage plots [merged_df2]
-# Count
-# Diversity
-# Average stability dist
-# Avergae affinity dist: optional
-#########################################################
-#=======
-# output
-#=======
-# outdir_images = paste0("~/git/Writing/thesis/images/results/"
-#                        , tolower(gene), "/")
-# cat("plots will output to:", outdir_images)
-#########################################################
-
-#===============
-#Quick numbers checks
-#===============
-nsample_lin = merged_df2[merged_df2$lineage%in%c("L1", "L2", "L3", "L4"),]
-
-if ( all(table(nsample_lin$sensitivity)== table(nsample_lin$mutation_info_labels)) ){
-  cat("\nTotal no. of samples belonging to L1-l4 for", gene,":", nrow(nsample_lin)
-      , "\nCounting R and S samples")
-  if( sum(table(nsample_lin$sensitivity)) ==  nrow(nsample_lin) ){
-    cat("\nPASSNumbers cross checked:")
-    print(table(nsample_lin$sensitivity))
-  }
-}else{
-  stop("Abort: Numbers mismatch. Please check")
-}
-########################################################################
-###################################################
-#                  Lineage barplots               #
-###################################################
-my_xats = 8 # x axis text size # were  25
-my_yats = 8# y axis text sized_lab_size
-my_xals = 8 # x axis label size
-my_yals = 8 # y axis label size
-my_lls  = 8 # legend label size
-d_lab_size = 2.3
-#===============================
-# lineage sample and SNP count
-#===============================
-lin_countP = lin_count_bp(lf_data = lineage_dfL[['lin_lf']]
-             , all_lineages = F
-             , x_categ = "sel_lineages"
-             , y_count = "p_count"
-             , use_lineages = c("L1", "L2", "L3", "L4")
-             , bar_fill_categ = "count_categ"
-             , display_label_col = "p_count"
-             , bar_stat_stype = "identity"
-             , d_lab_size = d_lab_size
-             , d_lab_col = "black"
-             , my_xats = my_xats # x axis text size
-             , my_yats = my_yats # y axis text sized_lab_size
-             , my_xals = my_xals # x axis label size
-             , my_yals = my_yals # y axis label size
-             , my_lls  = my_lls # legend label size
-             , bar_col_labels =  c("nsSNPs", "Total Samples")
-             , bar_col_values = c("grey50", "gray75")
-             , bar_leg_name = ""
-             , leg_location = "top"
-             , y_log10 = F
-             , y_scale_percent = FALSE
-             , y_label = c("Count")
-             )
-lin_countP
-#===============================
-# lineage SNP diversity count
-#===============================
-lin_diversityP = lin_count_bp_diversity(lf_data = lineage_dfL[['lin_wf']]
-                              , x_categ = "sel_lineages"
-                              , y_count = "snp_diversity"
-                              #, all_lineages = F
-                              , use_lineages = c("L1", "L2", "L3", "L4")
-                              , display_label_col = "snp_diversity_f"
-                              , bar_stat_stype = "identity"
-                              , x_lab_angle = 90
-                              , d_lab_size = d_lab_size
-                              , my_xats = my_xats # x axis text size
-                              , my_yats = my_yats # y axis text sized_lab_size
-                              , my_xals = my_xals # x axis label size
-                              , my_yals = my_yals # y axis label size
-                              , my_lls  = my_lls # legend label size
-                              , y_log10 = F
-                              , y_scale_percent = F
-                              , leg_location = "top"
-                              , y_label = "Percent" #"SNP diversity"
-                              , bp_plot_title = "nsSNP diversity"
-                              , title_colour = "black" #"chocolate4"
-                              , subtitle_text = NULL
-                              , sts = 10
-                              , subtitle_colour = "#350E20FF")
-lin_diversityP
-
-
-###################################################
-#                   Stability dist                #
-###################################################
-# scaled_cols_stability = c("duet_scaled"       
-#                           , "deepddg_scaled"   
-#                           , "ddg_dynamut2_scaled"
-#                           , "foldx_scaled"
-#                           , "avg_stability_scaled")
-
-my_ats = 8 # x axis text size # were  25
-my_als = 8# y axis text sized_lab_size
-my_leg_ts = 8 # x axis label size
-my_leg_title = 8 # y axis label size
-my_strip_ts  = 8 #
-
-
-my_xlabel = paste0("Average stability ", "(", stability_suffix, ")"); my_xlabel
-#plotdf = merged_df2[merged_df2$lineage%in%c("L1", "L2", "L3", "L4"),]
-
-linP_dm_om = lineage_distP(merged_df2
-                           , with_facet = F
-                           , x_axis = "avg_stability_scaled"
-                           , y_axis = "lineage_labels"
-                           , x_lab = my_xlabel
-                           , use_lineages = c("L1", "L2", "L3", "L4")
-                           #, fill_categ = "mutation_info_orig", fill_categ_cols = c("#E69F00", "#999999")
-                           , fill_categ = "sensitivity"
-                           , fill_categ_cols = c("red", "blue")
-                           , label_categories = c("Resistant", "Sensitive")
-                           , leg_label = "Mutation group"
-                           , my_ats = my_ats # axis text size
-                           , my_als = my_als # axis label size
-                           , my_leg_ts = my_leg_ts
-                           , my_leg_title = my_leg_title
-                           , my_strip_ts = my_strip_ts
-                           , alpha = 0.56
-)
-
-linP_dm_om
-
-###################################################
-#                 Affinity dist [OPTIONAL]        #
-###################################################
-# scaled_cols_affinity = c("affinity_scaled" 
-#                          , "mmcsm_lig_scaled" 
-#                          , "mcsm_ppi2_scaled" 
-#                          , "mcsm_na_scaled"
-#                          , "avg_lig_affinity_scaled")
-
-# lineage_distP(merged_df2
-#               , with_facet = F
-#               , x_axis = "avg_lig_affinity_scaled"
-#               , y_axis = "lineage_labels"
-#               , x_lab = my_xlabel
-#               , use_lineages = c("L1", "L2", "L3", "L4")
-#               #, fill_categ = "mutation_info_orig", fill_categ_cols = c("#E69F00", "#999999")
-#               , fill_categ = "sensitivity"
-#               , fill_categ_cols = c("red", "blue")
-#               , label_categories = c("Resistant", "Sensitive")
-#               , leg_label = "Mutation group"
-#               , my_ats = 22 # axis text size
-#               , my_als = 22 # axis label size
-#               , my_leg_ts = 22
-#               , my_leg_title = 22
-#               , my_strip_ts = 22
-#               , alpha = 0.56
-# )

scripts/plotting/plotting_thesis/linage_bp_dist_layout.R

@@ -1,54 +0,0 @@
-#!/usr/bin/env Rscript  
-source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/linage_bp_dist.R")
-###########################################
-# TASK: generate plots for lineage
-# Individual plots in 
-#lineage_bp_both.R
-#linage_dist_ens_stability.R
-###########################################
-# svg
-# linPlots_combined = paste0(outdir_images
-#                         , tolower(gene)
-#                         ,"_linP_combined.svg")
-# 
-# cat("\nOutput plot:", linPlots_combined)
-# svg(linPlots_combined, width = 18, height = 12)
-# 
-# cowplot::plot_grid(
-#   cowplot::plot_grid(lin_countP, lin_diversityP
-#                      , nrow = 2
-#                      , rel_heights = c(1.2,1)
-#                      , labels = "AUTO"
-#                      , label_size = my_label_size),
-#   NULL,
-#   linP_dm_om,
-#   nrow = 1,
-#   labels = c("", "", "C"),
-#   label_size = my_label_size,
-#   rel_widths = c(35, 3, 52)
-# )
-# dev.off()
-
-# png
-my_label_size = 12
-linPlots_combined = paste0(outdir_images
-                           , tolower(gene)
-                           ,"_linP_combined.png")
-
-cat("\nOutput plot:", linPlots_combined)
-png(linPlots_combined, width = 9, height = 6, units = "in" ,res = 300)
-
-cowplot::plot_grid(
-  cowplot::plot_grid(lin_countP, lin_diversityP
-                     , nrow = 2
-                     , rel_heights = c(1.2,1)
-                     , labels = "AUTO"
-                     , label_size = my_label_size),
-  NULL,
-  linP_dm_om,
-  nrow = 1,
-  labels = c("", "", "C"),
-  label_size = my_label_size,
-  rel_widths = c(35, 3, 52)
-)
-dev.off()