added separate scripts for layout for convinience

scripts/plotting/plotting_thesis/dm_om_plots_layout.R

@@ -0,0 +1,163 @@
+# source dm_om_plots.R
+#============
+# 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
+                         #, distanceP_na
+                         , 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
+                                          #, mcsmnaP
+                                          , 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()