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added DCS to alr config

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Tanushree Tunstall 2022-08-27 16:36:35 +01:00
parent c6f5a446c3
commit 927ab850a8
2 changed files with 1 additions and 178 deletions
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2
config/alr.R
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@ -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

177
scripts/plotting/plotting_thesis/alr/dm_om_plots_layout_alr.R
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@ -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()