added katg tables

config/katg.R

@@ -106,7 +106,7 @@ cat("\n==================================================="
 aa_pos_lig1 = aa_pos_hem
 aa_pos_lig2 = NULL
 aa_pos_lig3 = NULL
-tile_map=data.frame(tile=c("INH","HAEM"),
+tile_map=data.frame(tile=c("INH","HEME"),
                     tile_colour=c("green","darkslategrey"))
 
 

scripts/mut_electrostatic_changes.py

@@ -71,8 +71,8 @@ if not outdir:
 # input
 #=======
 #in_filename  = 'merged_df3.csv'
-#in_filename  = gene.lower() + '_complex_mcsm_norm.csv'
+in_filename  = gene.lower() + '_complex_mcsm_norm.csv'
-in_filename  = gene.lower() + '_complex_mcsm_norm_SRY.csv' # gid
+#in_filename  = gene.lower() + '_complex_mcsm_norm_SRY.csv' # gid
 infile_merged_df3 = outdir + '/' + in_filename
 print('Input file: ', infile_merged_df3
       , '\n============================================================')
@@ -217,4 +217,4 @@ print('Total no. of mutations: ', total_muts
       , '\nTotal no. of unchanged muts: ', no_change_muts.mut_count.sum() 
       , '\n=======================================================')  
 #%% end of script
-#=======================================================================
+#=======================================================================

scripts/plotting/plotting_thesis/alr/alr_appendix_tables.R

@@ -15,7 +15,6 @@ geneL_na_v2   = c("gid")
 geneL_ppi2    = c("alr", "embb", "katg", "rpob")
 geneL_both    = c("rpob")
 
-
 if (tolower(gene)%in%geneL_na_v2) {
   gene_colnames = c("mcsm_na_affinity", "mcsm_na_outcome")
 }
@@ -200,6 +199,7 @@ colsNames_to_output_nca = c("position"
                              #, paste0("NA-Dist (", angstroms_symbol, ")")
                              #, paste0("mCSM-NA (", delta_symbol,delta_symbol,"G)")
                              #, "mCSM-NA outcome"
+                             
                              , paste0("PPI-Dist (", angstroms_symbol, ")")
                              , paste0("mCSM-PPI (", delta_symbol,delta_symbol,"G)")
                              , "mCSM-PPI outcome"
@@ -226,7 +226,7 @@ table(Out_df_ncaS$plp_site)
 #----------------------
 Out_ncaT = paste0(outdir_stats
                    , tolower(gene)
-                   , "_na_muts.csv")
+                   , "_ppi2_muts.csv")
 
 cat("Output of NA muts:", Out_ncaT )
 write.csv(Out_df_ncaS, Out_ncaT, row.names = FALSE)

scripts/plotting/plotting_thesis/dm_om_plots.R

@@ -32,6 +32,7 @@ table(genomics_dataP$param_type)
 
 genomicsP = lf_bp2(genomics_dataP
                    #, p_title = ""
+                   , dot_transparency = 0.1 #0.3 default
                    , violin_quantiles = c(0.5), monochrome = F)
 
 genomicsP

scripts/plotting/plotting_thesis/gid/gid_appendix_tables.R

@@ -349,7 +349,7 @@ if (tolower(gene)%in%geneL_ppi2 ){
   
   # add cols
   mut_h_ppi2_dd$mutational_effect = "Most Destabilising for PPI affinity"
-  mut_h_ppi2_dd$mutational_effect = "Most Stabilising for PPI affinity"
+  mut_h_ppi2_ss$mutational_effect = "Most Stabilising for PPI affinity"
   
   if (identical(colnames(mut_h_ppi2_dd), colnames(mut_h_ppi2_ss)) ){
     cat("\nPass 1: ppi2")

scripts/plotting/plotting_thesis/katg/dm_om_plots_layout_katg.R

@@ -1,176 +0,0 @@
-# source dm_om_plots.R
-source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/dm_om_plots.R")
-
-##### plots to combine ####
-duetP
-foldxP
-deepddgP
-dynamut2P
-genomicsP
-consurfP
-proveanP
-snap2P
-mcsmligP
-mcsmlig2P
-mcsmppi2P
-
-# Plot labels
-tit1 = "Stability changes"
-tit2 = "Genomic measure"
-tit3 = "Distance to partners"
-tit4 = "Evolutionary Conservation"
-tit5 = "Affinity changes"
-pt_size = 30
-
-theme_georgia <- function(...) {
-  theme_gray(base_family = "sans", ...) + 
-    theme(plot.title = element_text(face = "bold"))
-}
-
-
-title_theme <- calc_element("plot.title", theme_georgia())
-
-pt1 = ggdraw() + 
-  draw_label(
-    tit1,
-    fontfamily = title_theme$family,
-    fontface = title_theme$face,
-    #size = title_theme$size
-    size = pt_size
-  )
-
-pt2 = ggdraw() + 
-  draw_label(
-    tit2,
-    fontfamily = title_theme$family,
-    fontface = title_theme$face,
-    size = pt_size
-  )
-
-pt3 = ggdraw() + 
-  draw_label(
-    tit3,
-    fontfamily = title_theme$family,
-    fontface = title_theme$face,
-    size = pt_size
-  )
-
-pt4 = ggdraw() + 
-  draw_label(
-    tit4,
-    fontfamily = title_theme$family,
-    fontface = title_theme$face,
-    size = pt_size
-  )
-
-
-pt5 = ggdraw() + 
-  draw_label(
-    tit5,
-    fontfamily = title_theme$family,
-    fontface = title_theme$face,
-    size = pt_size
-  )
-
-#======================
-# Output plot function
-#======================
-OutPlot_dm_om = function(x){
-  
-  # dist b/w plot title and plot
-  relH_tp = c(0.08, 0.92)
-  
-  my_label_size = 25
-  #----------------
-  # Top panel
-  #----------------
-  top_panel = cowplot::plot_grid(
-    cowplot::plot_grid(pt1, 
-                       cowplot::plot_grid(duetP, foldxP, deepddgP, dynamut2P
-                                          , nrow = 1
-                                          , labels = c("A", "B", "C", "D")
-                                          , label_size = my_label_size)
-                       , ncol = 1
-                       , rel_heights = relH_tp
-    ),
-    NULL,
-    cowplot::plot_grid(pt2, 
-                       cowplot::plot_grid(genomicsP
-                                          , nrow = 1
-                                          , labels = c("E")
-                                          , label_size = my_label_size)
-                       , ncol = 1
-                       , rel_heights = relH_tp
-    ),
-    NULL,
-    cowplot::plot_grid(pt3, 
-                       cowplot::plot_grid( #distanceP
-                         distanceP_lig
-                         , distanceP_ppi2
-                         , nrow = 1
-                         , labels = c("F", "G")
-                         , label_size = my_label_size)
-                       , ncol = 1
-                       , rel_heights = relH_tp
-    ),
-    nrow = 1,
-    rel_widths = c(2/7, 0.1/7, 0.5/7, 0.1/7,  1/7)
-  )
-  
-  #----------------
-  # Bottom panel
-  #----------------
-  bottom_panel = cowplot::plot_grid(
-    cowplot::plot_grid(pt4, 
-                       cowplot::plot_grid(consurfP, proveanP, snap2P
-                                          , nrow = 1
-                                          , labels = c("H", "I", "J")
-                                          , label_size = my_label_size)
-                       , ncol = 1
-                       , rel_heights =relH_tp
-    ),NULL,
-    cowplot::plot_grid(pt5, 
-                       cowplot::plot_grid(mcsmligP
-                                          , mcsmlig2P
-                                          , mcsmppi2P
-                                          , nrow = 1
-                                          , labels = c("K", "L", "M")
-                                          , label_size = my_label_size)
-                       , ncol = 1
-                       , rel_heights = relH_tp
-    ),NULL,
-    nrow = 1, 
-    rel_widths = c(3/6,0.1/6,3/6, 0.1/6 )
-  )
-  
-  #-------------------------------
-  # combine: Top and Bottom panel
-  #-------------------------------
-  cowplot::plot_grid (top_panel, bottom_panel
-                      , nrow =2
-                      , rel_widths = c(1, 1)
-                      , align = "hv")
-}
-
-#=====================
-# OutPlot: svg and png
-#======================
-dm_om_combinedP =  paste0(outdir_images
-                          ,tolower(gene)
-                          ,"_dm_om_all.svg")
-
-cat("DM OM plots with stats:", dm_om_combinedP)
-svg(dm_om_combinedP, width = 32, height = 18)
-
-OutPlot_dm_om()
-dev.off()
-
-
-dm_om_combinedP_png =  paste0(outdir_images
-                              ,tolower(gene)
-                              ,"_dm_om_all.png")
-cat("DM OM plots with stats:", dm_om_combinedP_png)
-png(dm_om_combinedP_png, width = 32, height = 18, units = "in", res = 300)
-
-OutPlot_dm_om()
-dev.off()

scripts/plotting/plotting_thesis/katg/gg_pairs_all_katg.R

@@ -1,4 +1,4 @@
-#source("~/git/LSHTM_analysis/config/embb.R")
+#source("~/git/LSHTM_analysis/config/katg.R")
 #source("~/git/LSHTM_analysis/scripts/plotting/plotting_colnames.R")
 #source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
 
@@ -53,7 +53,7 @@ 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/lineage_bp_dist_layout.R

@@ -1,5 +1,11 @@
 #!/usr/bin/env Rscript  
-source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/linage_bp_dist.R")
+source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/lineage_bp_dist.R")
+
+#=======
+# output
+#=======
+outdir_images = paste0("~/git/Writing/thesis/images/results/", tolower(gene), "/")
+cat("plots will output to:", outdir_images)
 ###########################################
 # TASK: generate plots for lineage
 # Individual plots in 
@@ -38,19 +44,19 @@ linPlots_combined = paste0(outdir_images
 cat("\nOutput plot:", linPlots_combined)
 png(linPlots_combined, width = 9, height = 6, units = "in" ,res = 300)
  
- cowplot::plot_grid(
+cowplot::plot_grid(
-   cowplot::plot_grid(lin_countP, lin_diversityP
+  cowplot::plot_grid(lin_countP, lin_diversityP,
-#                      , nrow = 2
+                     nrow = 2,
-#                      , rel_heights = c(1.2,1)
+                     rel_heights = c(1.2,1),
-#                      , labels = "AUTO"
+                     labels = "AUTO",
-#                      , label_size = my_label_size),
+                     label_size = my_label_size),
-#   NULL,
+  NULL,
-#   linP_dm_om,
+  linP_dm_om,
-#   nrow = 1,
+  nrow = 1,
-#   labels = c("", "", "C"),
+  labels = c("", "", "C"),
-#   label_size = my_label_size,
+  label_size = my_label_size,
-#   rel_widths = c(35, 3, 52)
+  rel_widths = c(35, 3, 52)
-# )
+)
-# dev.off()
+dev.off()