diff --git a/config/alr.R b/config/alr.R index b27ae4a..22037b7 100644 --- a/config/alr.R +++ b/config/alr.R @@ -153,7 +153,7 @@ aa_pos_lig1 = aa_pos_plp aa_pos_lig2 = NULL aa_pos_lig3 = NULL -tile_map=data.frame(tile=c("ALR","PLP"), +tile_map=data.frame(tile=c("DCS","PLP"), tile_colour=c("green","navyblue")) #darkslategrey diff --git a/scripts/plotting/plotting_thesis/alr/dm_om_plots_layout_alr.R b/scripts/plotting/plotting_thesis/alr/dm_om_plots_layout_alr.R deleted file mode 100644 index cab13ae..0000000 --- a/scripts/plotting/plotting_thesis/alr/dm_om_plots_layout_alr.R +++ /dev/null @@ -1,177 +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()