added separate scripts for layout for convinience
This commit is contained in:
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d78b072732
commit
cd86fcf8e8
6 changed files with 468 additions and 78 deletions
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@ -326,15 +326,13 @@ snap2P = stability_count_bp(plotdf = df3
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#
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# dev.off()
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#####################################################################
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# LAYOUT
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my_label_size = 25
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#ratio 11.69 by 8.27
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w = 8.27*2
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h = 11.69*2
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#============
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# Plot labels
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#============
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tit1 = "Stability outcome"
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tit2 = "Affinity outcome"
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tit3 = "Conservation outcome"
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pt_size = 30
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theme_georgia <- function(...) {
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@ -351,7 +349,7 @@ pt1 = ggdraw() +
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fontfamily = title_theme$family,
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fontface = title_theme$face,
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#size = title_theme$size
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size = 30
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size = pt_size
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)
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pt2 = ggdraw() +
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@ -359,7 +357,7 @@ pt2 = ggdraw() +
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tit2,
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fontfamily = title_theme$family,
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fontface = title_theme$face,
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size = 30
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size = pt_size
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)
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pt3 = ggdraw() +
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@ -367,7 +365,7 @@ pt3 = ggdraw() +
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tit3,
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fontfamily = title_theme$family,
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fontface = title_theme$face,
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size = 30
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size = pt_size
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)
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# extract common legend
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@ -376,9 +374,11 @@ common_legend_outcome = get_legend(mLigP +
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theme(legend.position = "top"))
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#=============
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# Output plot
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#=============
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my_label_size = 25
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#======================
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# Output plot function
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#======================
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OutPlotBP = function(x){
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cowplot::plot_grid(
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cowplot::plot_grid(pt1,
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@ -422,25 +422,35 @@ cowplot::plot_grid(
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)
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}
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#=====================
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# OutPlot: svg and png
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#======================
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#ratio 11.69 by 8.27
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w = 8.27*2
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h = 11.69*2
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#svg
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bp_all_CLP = paste0(outdir_images
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,tolower(gene)
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,"_bp_all_CL.svg"); print(paste0("plot filename:", bp_all_CLP))
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bp_all_CLP_png = paste0(outdir_images
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,tolower(gene)
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,"_bp_all_CL.png"); print(paste0("plot filename:", bp_all_CLP_png))
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,"_bp_all_CL.svg")
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cat(paste0("plot filename:", bp_all_CLP))
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svg(bp_all_CLP, width = w, height = h)
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OutPlotBP()
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dev.off()
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#png
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bp_all_CLP_png = paste0(outdir_images
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,tolower(gene)
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,"_bp_all_CL.png")
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cat(paste0("plot filename:", bp_all_CLP_png))
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png(bp_all_CLP_png, width = w, height = h, units = "in", res = 300 )
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OutPlotBP()
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dev.off()
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#####################################################################
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#===============================================================
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#####################################################################
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# ------------------------------
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# bp site site count: ALL
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# <10 Ang ligand
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@ -505,7 +515,6 @@ cowplot::plot_grid(posC_all, posC_lig, posC_ppi2
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#, posC_na
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, nrow = 1
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, ncol = 3
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#, labels = c("(a)", "(b)", "(c)", "(d)")
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, labels = "AUTO"
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, label_size = my_label_size)
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@ -1,27 +1,198 @@
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#!/usr/bin/env Rscript
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#########################################################
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#main script that generates plot objects:
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#source("basic_barplots.R")
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#########################################################
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# source basic_barplots.R
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#============
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# Plot labels
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#============
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tit1 = "Stability outcome"
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tit2 = "Affinity outcome"
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tit3 = "Conservation outcome"
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pt_size = 30
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theme_georgia <- function(...) {
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theme_gray(base_family = "sans", ...) +
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theme(plot.title = element_text(face = "bold"))
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}
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title_theme <- calc_element("plot.title", theme_georgia())
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pt1 = ggdraw() +
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draw_label(
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tit1,
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fontfamily = title_theme$family,
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fontface = title_theme$face,
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#size = title_theme$size
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size = pt_size
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)
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pt2 = ggdraw() +
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draw_label(
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tit2,
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fontfamily = title_theme$family,
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fontface = title_theme$face,
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size = pt_size
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)
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pt3 = ggdraw() +
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draw_label(
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tit3,
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fontfamily = title_theme$family,
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fontface = title_theme$face,
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size = pt_size
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)
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# extract common legend
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common_legend_outcome = get_legend(mLigP +
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guides(color = guide_legend(nrow = 1)) +
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theme(legend.position = "top"))
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my_label_size = 25
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#======================
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# Output plot function
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#======================
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OutPlotBP = function(x){
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cowplot::plot_grid(
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cowplot::plot_grid(pt1,
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common_legend_outcome,
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cowplot::plot_grid( duetP, foldxP
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, deepddgP, dynamut2P
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, nrow = 2
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, ncol = 2
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, labels = c("A", "B", "C","D")
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, label_size = my_label_size
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)
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, ncol = 1
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, rel_heights = c(7, 3, 90)),
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cowplot::plot_grid(pt2,
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cowplot::plot_grid(mLigP, mmLigP, ppi2P
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, nrow = 1
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, ncol = 3
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, labels = c("E","F", "G")
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, label_size = my_label_size
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)
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, ncol = 1
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, rel_heights = c(1, 9)),
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cowplot::plot_grid(pt3,
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cowplot::plot_grid(consurfP, proveanP, snap2P
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, nrow = 1
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, ncol = 3
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, labels = c("H", "I", "J")
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, labels_x = 0.2
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, label_size = my_label_size
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, rel_widths = c(0.2, 0.2, 0.2)
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)
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, ncol = 1
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, rel_heights = c(0.07, 0.93)
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),
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nrow = 3,
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rel_heights = c(0.58, 0.25, 0.27),
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align = "hv"
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)
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}
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#=======================================================================
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#=======
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# output
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#=======
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outdir_images = paste0("~/git/Writing/thesis/images/results/"
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, tolower(gene), "/")
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cat("plots will output to:", outdir_images)
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#=====================
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# OutPlot: svg and png
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#======================
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#ratio 11.69 by 8.27
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w = 8.27*2
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h = 11.69*2
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df_colname = "duet_outcome"
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#svg
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bp_all_CLP = paste0(outdir_images
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,tolower(gene)
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,"_bp_all_CL.svg")
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cat(paste0("plot filename:", bp_all_CLP))
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OutPlot_count = ggplot(df3, aes_string(x = df_colname)) +
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geom_bar(aes(fill = eval(parse(text = df_colname)))
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, show.legend = TRUE) +
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geom_label(stat = "count"
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, aes(label = ..count..)
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, color = "black"
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, show.legend = FALSE
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, size = geom_ls)
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svg(bp_all_CLP, width = w, height = h)
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OutPlotBP()
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dev.off()
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#png
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bp_all_CLP_png = paste0(outdir_images
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,tolower(gene)
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,"_bp_all_CL.png")
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cat(paste0("plot filename:", bp_all_CLP_png))
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png(bp_all_CLP_png, width = w, height = h, units = "in", res = 300 )
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OutPlotBP()
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dev.off()
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#####################################################################
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#####################################################################
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# ------------------------------
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# bp site site count: ALL
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# <10 Ang ligand
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# ------------------------------
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posC_all = site_snp_count_bp(plotdf = df3
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, df_colname = "position"
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, xaxis_title = "Number of nsSNPs"
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, yaxis_title = "Number of Sites"
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, subtitle_size = 20)
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# ------------------------------
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# bp site site count: mCSM-lig
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# < 10 Ang ligand
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# ------------------------------
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common_bp_title = paste0("Sites <", DistCutOff, angstroms_symbol)
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posC_lig = site_snp_count_bp(plotdf = df3_lig
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, df_colname = "position"
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, xaxis_title = "Number of nsSNPs"
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, yaxis_title = "Number of Sites"#+ annotate("text", x = 1.5, y = 2.2, label = "Text No. 1")
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, subtitle_text = paste0(common_bp_title, " ligand")
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, subtitle_size = 20
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, subtitle_colour = subtitle_colour)
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# ------------------------------
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# bp site site count: ppi2
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# < 10 Ang interface
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# ------------------------------
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posC_ppi2 = site_snp_count_bp(plotdf = df3_ppi2
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, df_colname = "position"
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, xaxis_title = "Number of nsSNPs"
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, yaxis_title = "Number of Sites"
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, subtitle_text = paste0(common_bp_title, " interface")
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, subtitle_size = 20
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, subtitle_colour = subtitle_colour)
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# ------------------------------
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#FIXME: bp site site count: na
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# < 10 Ang TBC
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# ------------------------------
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# posC_na = site_snp_count_bp(plotdf = df3_na
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# , df_colname = "position"
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# , xaxis_title = ""
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# , yaxis_title = "")
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#===========================
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# output: SITE SNP count:
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# all + affinity
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#==========================
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my_label_size = 25
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pos_count_combined_CLP = paste0(outdir_images
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,tolower(gene)
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,"_pos_count_PS_AFF.svg")
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svg(pos_count_combined_CLP, width = 20, height = 5.5)
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print(paste0("plot filename:", pos_count_combined_CLP))
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cowplot::plot_grid(posC_all, posC_lig, posC_ppi2
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#, posC_na
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, nrow = 1
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, ncol = 3
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, labels = "AUTO"
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, label_size = my_label_size)
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dev.off()
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#===============================================================
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@ -22,7 +22,7 @@ genomics_param = c("Log10(MAF)")
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dist_genP = lf_bp2(lf_dist_genP
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#, p_title
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, violin_quantiles = c(0.5), monochrome = F)
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#dist_genP
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#-------------------
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# Genomics data plot
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#-------------------
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@ -42,12 +42,18 @@ wilcox.test(wf_dist_genP$`Log10(MAF)`[wf_dist_genP$mutation_info_labels=="R"]
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tapply(wf_dist_genP$`Log10(MAF)`, wf_dist_genP$mutation_info_labels, summary)
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#---------------------------------------
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# Distance data plot: not genomics data
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#---------------------------------------
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#-------------------
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# Distance data plot:
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#--------------------
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# not genomics
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dist_dataP = lf_dist_genP[!lf_dist_genP$param_type%in%genomics_param,]
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#dist_dataP$param_type = factor(dist_dataP$param_type)
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dist_dataP$param_type = factor(dist_dataP$param_type)
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table(dist_dataP$param_type)
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levels(dist_dataP$param_type)
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# relevel factor to control ordering of appearance of plot
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dist_dataP$param_type <-relevel(dist_dataP$param_type, "Lig Dist(Å)" )
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table(dist_dataP$param_type)
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levels(dist_dataP$param_type)
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distanceP = lf_bp2(dist_dataP
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#, p_title = ""
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@ -66,6 +72,55 @@ tapply(wf_dist_genP$`PPI Dist(Å)`, wf_dist_genP$mutation_info_labels, summary)
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tapply(wf_dist_genP$`Lig Dist(Å)`, wf_dist_genP$mutation_info_labels, summary)
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#-------------------
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# Distance data plot: LigDist
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#--------------------
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levels(dist_dataP$param_type)[[1]]
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#Lig Dist(Å), PPI Dist(Å)
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dist_data_lig = dist_dataP[dist_dataP$param_type%in%c(levels(dist_dataP$param_type)[[1]]),]
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dist_data_lig$param_type = factor(dist_data_lig$param_type)
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table(dist_data_lig$param_type)
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levels(dist_data_lig$param_type)
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distanceP_lig = lf_bp2(dist_data_lig
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#, p_title = ""
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, violin_quantiles = c(0.5), monochrome = F)
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distanceP_lig
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if (tolower(gene)%in%geneL_ppi2){
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#-------------------
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# Distance data plot: LigDist
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#--------------------
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levels(dist_dataP$param_type)[[2]]
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#Lig Dist(Å), PPI Dist(Å)
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dist_data_ppi2 = dist_dataP[dist_dataP$param_type%in%c(levels(dist_dataP$param_type)[[2]]),]
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dist_data_ppi2$param_type = factor(dist_data_ppi2$param_type)
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table(dist_data_ppi2$param_type)
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levels(dist_data_ppi2$param_type)
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distanceP_ppi2 = lf_bp2(dist_data_ppi2
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#, p_title = ""
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, violin_quantiles = c(0.5), monochrome = F)
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distanceP_ppi2
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}
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if (tolower(gene)%in%geneL_na){
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#-------------------
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# Distance data plot: NADist
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#--------------------
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levels(dist_dataP$param_type)[[3]]
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#Lig Dist(Å), PPI Dist(Å)
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dist_data_na = dist_dataP[dist_dataP$param_type%in%c(levels(dist_dataP$param_type)[[3]]),]
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dist_data_na$param_type = factor(dist_data_na$param_type)
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table(dist_data_na$param_type)
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levels(dist_data_na$param_type)
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distanceP_na = lf_bp2(dist_data_na
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#, p_title = ""
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, violin_quantiles = c(0.5), monochrome = F)
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distanceP_na
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}
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#==============
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# Plot:DUET
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#==============
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@ -234,35 +289,27 @@ if (tolower(gene)%in%geneL_na){
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######################################
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# Outplot with stats
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######################################
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outdir_images = paste0("~/git/Writing/thesis/images/results/", tolower(gene), "/")
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dm_om_combinedP = paste0(outdir_images
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,tolower(gene)
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,"_dm_om_all.svg" )
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cat("DM OM plots with stats:", dm_om_combinedP)
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svg(dm_om_combinedP, width = 32, height = 18)
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cowplot::plot_grid(
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cowplot::plot_grid(duetP, foldxP, deepddgP, dynamut2P, genomicsP, distanceP
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, nrow=1
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, rel_widths = c(1/7, 1/7,1/7,1/7, 1/7, 1.75/7)),
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#, rel_widths = c(1/8, 1/8,1/8,1/8, 1/8, 2.75/8)), # for 3 distances
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cowplot::plot_grid(consurfP, proveanP, snap2P
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, mcsmligP
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, mcsmlig2P
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, mcsmppi2P
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#, mcsmnaP
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, nrow=1),
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nrow=2)
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dev.off()
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#foo = lf_consurfP
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# proveanP = lf_bp2(lf_proveanP, colour_categ = "mutation_info_labels"
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# , p_title = paste0("Evolutionary conservation")
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# , dot_transparency = 1
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# , violin_quantiles = c(0.5), monochrome = F)
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# outdir_images = paste0("~/git/Writing/thesis/images/results/", tolower(gene), "/")
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#
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# proveanP
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# dm_om_combinedP = paste0(outdir_images
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# ,tolower(gene)
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# ,"_dm_om_all.svg" )
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#
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# cat("DM OM plots with stats:", dm_om_combinedP)
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# svg(dm_om_combinedP, width = 32, height = 18)
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# cowplot::plot_grid(
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# cowplot::plot_grid(duetP, foldxP, deepddgP, dynamut2P, genomicsP, distanceP
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# , nrow=1
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# , rel_widths = c(1/7, 1/7,1/7,1/7, 1/7, 1.75/7)),
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# #, rel_widths = c(1/8, 1/8,1/8,1/8, 1/8, 2.75/8)), # for 3 distances
|
||||
# cowplot::plot_grid(consurfP, proveanP, snap2P
|
||||
# , mcsmligP
|
||||
# , mcsmlig2P
|
||||
# , mcsmppi2P
|
||||
# #, mcsmnaP
|
||||
# , nrow=1),
|
||||
# nrow=2)
|
||||
#
|
||||
# dev.off()
|
||||
|
||||
|
||||
|
|
|
|||
163
scripts/plotting/plotting_thesis/dm_om_plots_layout.R
Normal file
163
scripts/plotting/plotting_thesis/dm_om_plots_layout.R
Normal file
|
|
@ -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()
|
||||
Loading…
Add table
Add a link
Reference in a new issue