From cd9b1ad245bb5bee83990e1a1a224986526847d6 Mon Sep 17 00:00:00 2001
From: Tanushree Tunstall <tanu@tunstall.in>
Date: Tue, 16 Aug 2022 14:45:31 +0100
Subject: [PATCH] stability and cons revised bp out

---
 .../plotting_thesis/basic_barplots2.R         | 114 +++++++++
 .../basic_barplots_layout_v2.R                | 233 ++++++++----------
 2 files changed, 222 insertions(+), 125 deletions(-)

diff --git a/scripts/plotting/plotting_thesis/basic_barplots2.R b/scripts/plotting/plotting_thesis/basic_barplots2.R
index 3cccf5e..b75d049 100644
--- a/scripts/plotting/plotting_thesis/basic_barplots2.R
+++ b/scripts/plotting/plotting_thesis/basic_barplots2.R
@@ -321,6 +321,120 @@ sensP
 #   coord_flip() + scale_x_reverse()
 # sensP2
 
+##############################################################
+#===================
+# Stability
+#===================
+# duetP
+duetP = stability_count_bp(plotdf = df3
+                           , df_colname = "duet_outcome"
+                           , leg_title = "mCSM-DUET"
+                           #, label_categories = labels_duet
+                           , yaxis_title = "Number of nsSNPs"
+                           , leg_position = "none"
+                           , subtitle_text = "mCSM-DUET"
+                           , bar_fill_values = c("#F8766D", "#00BFC4")
+                           , subtitle_colour= "black"
+                           , sts = 10
+                           , lts = 8
+                           , ats = 12
+                           , als = 11
+                           , ltis = 11
+                           , geom_ls = 2.5
+)
+duetP
+
+# foldx
+foldxP = stability_count_bp(plotdf = df3
+                            , df_colname = "foldx_outcome"
+                            #, leg_title = "FoldX"
+                            #, label_categories = labels_foldx
+                            , yaxis_title = ""
+                            , leg_position = "none"
+                            , subtitle_text = "FoldX"
+                            , bar_fill_values = c("#F8766D", "#00BFC4")
+                            , sts = 10
+                            , lts = 8
+                            , ats = 12
+                            , als = 11
+                            , ltis = 11
+                            , geom_ls = 2.5
+)
+
+
+# deepddg
+deepddgP = stability_count_bp(plotdf = df3
+                              , df_colname = "deepddg_outcome"
+                              #, leg_title = "DeepDDG"
+                              #, label_categories = labels_deepddg
+                              , yaxis_title = ""
+                              , leg_position = "none"
+                              , subtitle_text = "DeepDDG"
+                              , bar_fill_values = c("#F8766D", "#00BFC4")
+                              , sts = 10
+                              , lts = 8
+                              , ats = 12
+                              , als = 11
+                              , ltis = 11
+                              , geom_ls = 2.5
+)
+
+
+# deepddg
+dynamut2P = stability_count_bp(plotdf = df3
+                               , df_colname = "ddg_dynamut2_outcome"
+                               #, leg_title = "Dynamut2"
+                               #, label_categories = labels_ddg_dynamut2_outcome
+                               , yaxis_title = ""
+                               , leg_position = "none"
+                               , subtitle_text = "Dynamut2"
+                               , bar_fill_values = c("#F8766D", "#00BFC4")
+                               , sts = 10
+                               , lts = 8
+                               , ats = 12
+                               , als = 11
+                               , ltis = 11
+                               , geom_ls = 2.5
+)
+dynamut2P
+
+
+# provean
+proveanP = stability_count_bp(plotdf = df3
+                              , df_colname = "provean_outcome"
+                              #, leg_title = "PROVEAN"
+                              #, label_categories = labels_provean
+                              , yaxis_title = "Number of nsSNPs"
+                              , leg_position = "none" # top
+                              , subtitle_text = "PROVEAN"
+                              , bar_fill_values = c("#D01C8B", "#F1B6DA") # light pink and deep
+                              , sts = 10
+                              , lts = 8
+                              , ats = 12
+                              , als = 11
+                              , ltis = 11
+                              , geom_ls = 2.5
+)
+
+# snap2
+snap2P = stability_count_bp(plotdf = df3
+                            , df_colname = "snap2_outcome"
+                            #, leg_title = "SNAP2"
+                            #, label_categories = labels_snap2
+                            , yaxis_title = ""
+                            , leg_position = "none" # top
+                            , subtitle_text = "SNAP2"
+                            , bar_fill_values = c("#D01C8B", "#F1B6DA") # light pink and deep
+                            , sts = 10
+                            , lts = 8
+                            , ats = 12
+                            , als = 11
+                            , ltis = 11
+                            , geom_ls = 2.5)
+
+
+##############################################################
+
 ##############################
 # FIXME for other genes: ATTEMPTED to derive numbers
 ##############################
diff --git a/scripts/plotting/plotting_thesis/basic_barplots_layout_v2.R b/scripts/plotting/plotting_thesis/basic_barplots_layout_v2.R
index 2265ced..77062b8 100644
--- a/scripts/plotting/plotting_thesis/basic_barplots_layout_v2.R
+++ b/scripts/plotting/plotting_thesis/basic_barplots_layout_v2.R
@@ -1,145 +1,127 @@
+duetP
+foldxP
+deepddgP
+dynamut2P
+proveanP
+snap2P
+
 mLigP
 mmLigP
 posC_lig
 ppi2P
 posC_ppi2
 peP
-
-
+sensP
+#========================
+# Common title settings
+#=========================
 theme_georgia <- function(...) {
   theme_gray(base_family = "sans", ...) + 
     theme(plot.title = element_text(face = "bold"))
 }
 title_theme <- calc_element("plot.title", theme_georgia())
 
-
 ###############################################################
 common_bp_title = paste0("Sites <", DistCutOff, angstroms_symbol)
 
-# extract common legend
+# extract common legends
+# lig affinity
 common_legend_outcome = get_legend(mLigP +
                                      guides(color = guide_legend(nrow = 1)) +
                                      theme(legend.position = "top"))
 
-# ###############################################################
-# #================================
-# # Lig Affinity: outcome + site
-# #================================
-# ligT = paste0(common_bp_title, " ligand")
-# lig_affT = ggdraw() +
-#   draw_label(
-#     ligT,
-#     fontfamily = title_theme$family,
-#     fontface = title_theme$face,
-#     #size = title_theme$size
-#     size = 8
-#   )
+# stability
+common_legend_outcome = get_legend(duetP +
+                                     guides(color = guide_legend(nrow = 1)) +
+                                     theme(legend.position = "top"))
+# conservation
+cons_common_legend_outcome = get_legend(snap2P +
+                                          guides(color = guide_legend(nrow = 1)) +
+                                          theme(legend.position = "top"))
+###################################################################
+#==================================
+# Stability+Consevation: COMBINE
+#==================================
+tt_size = 10
+#----------------------------
+# stability and consv title
+#----------------------------
+tt_size = 10
+tt_stab = ggdraw() + 
+  draw_label(
+    paste0("Stability outcome"),
+    fontfamily = title_theme$family,
+    fontface = title_theme$face,
+    #size = title_theme$size
+    size = tt_size
+  )
+
+tt_cons = ggdraw() + 
+  draw_label(
+    paste0("Conservation outcome"),
+    fontfamily = title_theme$family,
+    fontface = title_theme$face,
+    size = tt_size
+  )
+
+#----------------------
+# Output plot
+#-----------------------
+stab_cons_CLP =  paste0(outdir_images
+                        ,tolower(gene)
+                        ,"_stab_cons_BP_CLP.png")
+
+print(paste0("plot filename:", stab_cons_CLP))
+png(stab_cons_CLP, units = "in", width = 10, height = 5, res = 300 )
+
+cowplot::plot_grid(
+  cowplot::plot_grid(
+    cowplot::plot_grid(
+      tt_stab,
+      common_legend_outcome,
+      nrow = 2
+    ),
+    cowplot::plot_grid(
+      duetP, 
+      foldxP, 
+      deepddgP, 
+      dynamut2P,
+      nrow = 1,
+      labels = c("A", "B", "C", "D"),
+      label_size = 12),
+    nrow = 2,
+    rel_heights=c(1,10)
+  ),
+  NULL,
+  cowplot::plot_grid(
+    cowplot::plot_grid(
+      cowplot::plot_grid(
+        tt_cons,
+        cons_common_legend_outcome,
+        nrow = 2
+      ),
+      cowplot::plot_grid(
+        proveanP,
+        snap2P,
+        nrow=1, 
+        labels = c("E", "F"),
+        align = "hv"),
+      nrow = 2,
+      rel_heights = c(1, 10),
+      label_size = 12),
+    nrow=1
+  ),
+  rel_widths = c(2,0.15,1),
+  nrow=1
+)
+
+dev.off()
+
+#################################################################
+#=======================================
+# Affinity barplots: COMBINE ALL three
+#========================================
 
-# #-------------
-# # Outplot
-# #-------------
-# ligaffP =  paste0(outdir_images
-#                   ,tolower(gene)
-#                   ,"_lig_oc.png")
-# 
-# #svg(affP, width = 20, height = 5.5)
-# print(paste0("plot filename:", ligaffP))
-# png(ligaffP, units = "in", width = 6, height = 4, res = 300 )
-# cowplot::plot_grid(cowplot::plot_grid(lig_affT,common_legend_outcome,
-#                                       nrow = 2,
-#                                       rel_heights = c(1,1)
-# ), 
-# cowplot::plot_grid(mLigP, mmLigP, posC_lig
-#                    , nrow = 1
-#                    #, labels = c("A", "B", "C","D")
-#                    , rel_widths = c(1,1,1.8)
-#                    , align = "h"),
-# nrow = 2,
-# labels = c("A", ""),
-# label_size = 12,
-# rel_heights = c(1,8))
-# dev.off()
-# #############################################################
-# #================================
-# # PPI2 Affinity: outcome + site
-# #================================
-# ppi2T = paste0(common_bp_title, " PP-interface")
-# ppi2_affT = ggdraw() + 
-#   draw_label(
-#     ppi2T,
-#     fontfamily = title_theme$family,
-#     fontface = title_theme$face,
-#     #size = title_theme$size
-#     size = 8
-#   )
-# 
-# 
-# #-------------
-# # Outplot: PPI2
-# #-------------
-# ppiaffP =  paste0(outdir_images
-#                   ,tolower(gene)
-#                   ,"_ppi2_oc.png")
-# 
-# #svg(affP, width = 20, height = 5.5)
-# print(paste0("plot filename:", ppiaffP))
-# png(ppiaffP, units = "in", width = 6, height = 4, res = 300 )
-# 
-# 
-# cowplot::plot_grid(cowplot::plot_grid(ppi2_affT, common_legend_outcome,
-#                                       nrow = 2,
-#                                       rel_heights = c(1,1)), 
-#                    cowplot::plot_grid(ppi2P, posC_ppi2
-#                                       , nrow = 1
-#                                       , rel_widths = c(1.2,1.8)
-#                                       , align = "h"
-#                                       , label_size = my_label_size),
-#                    nrow = 2,
-#                    labels = c("B", ""),
-#                    label_size = 12,
-#                    rel_heights = c(1,8)
-# )
-# 
-# dev.off()
-# #############################################################
-#peP # pe counts
-#================================
-# PE + All position count
-#================================
-# peT_allT = ggdraw() +
-#   draw_label(
-#     paste0("All mutation sites"),
-#     fontfamily = title_theme$family,
-#     fontface = title_theme$face,
-#     #size = title_theme$size
-#     size = 8
-#   )
-# #------------------------
-# # Outplot: lig+ppi2+pe
-# #------------------------
-# pe_allCL =  paste0(outdir_images
-#                    ,tolower(gene)
-#                    ,"_pe_oc.png")
-# 
-# #svg(affP, width = 20, height = 5.5)
-# print(paste0("plot filename:", pe_allCL))
-# png(pe_allCL, units = "in", width = 6, height = 4, res = 300 )
-# 
-# 
-# cowplot::plot_grid(peT_allT,
-#                    cowplot::plot_grid(peP, posC_all
-#                                       , nrow = 1
-#                                       , rel_widths = c(1, 2)
-#                                       , align = "h"),
-#                    nrow = 2,
-#                    labels = c("C", "", ""),
-#                    label_size = 12,
-#                    rel_heights = c(1,8))
-# 
-# dev.off()
-#===========================================
-# COMBINE ALL three
-#==========================================
 ligT = paste0(common_bp_title, " ligand")
 lig_affT = ggdraw() +
   draw_label(
@@ -150,7 +132,9 @@ lig_affT = ggdraw() +
     size = 8
   )
 
-p1 = cowplot::plot_grid(cowplot::plot_grid(lig_affT,common_legend_outcome, nrow=2),
+p1 = cowplot::plot_grid(cowplot::plot_grid(lig_affT
+                                           , common_legend_outcome
+                                           , nrow=2),
                         cowplot::plot_grid(mLigP, mmLigP, posC_lig
                                            , nrow = 1
                                            , rel_widths = c(1,1,1.8)
@@ -217,7 +201,6 @@ mut_impact_CLP =  paste0(outdir_images
 print(paste0("plot filename:", mut_impact_CLP))
 png(mut_impact_CLP, units = "in", width = w, height = h, res = 300 )
 
-
 cowplot::plot_grid(p1, p2, p3
                    , nrow = 1
                    , labels = "AUTO"
@@ -270,5 +253,5 @@ print(paste0("plot filename:", sensCLP))
 png(sensCLP, units = "in", width = 1, height = 1, res = 300 )
 sensP
 dev.off()
-
+###########################################################