added separate scripts for layout for convinience
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d78b072732
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6 changed files with 468 additions and 78 deletions
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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
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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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#
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# dev.off()
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