updated corr_PS_LIG.R to output both styles of corr plots
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ea5d5bda44
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1 changed files with 105 additions and 38 deletions
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@ -59,10 +59,16 @@ cat(paste0("Variables imported:"
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corr_ps = "corr_PS.svg"
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corr_ps = "corr_PS.svg"
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plot_corr_ps = paste0(plotdir,"/", corr_ps)
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plot_corr_ps = paste0(plotdir,"/", corr_ps)
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corr_upper_ps = "corr_upper_PS.svg"
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plot_corr_upper_ps = paste0(plotdir,"/", corr_upper_ps)
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# LIG
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# LIG
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corr_lig = "corr_LIG.svg"
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corr_lig = "corr_LIG.svg"
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plot_corr_lig = paste0(plotdir,"/", corr_lig)
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plot_corr_lig = paste0(plotdir,"/", corr_lig)
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corr_upper_lig = "corr_upper_LIG.svg"
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plot_corr_upper_lig = paste0(plotdir,"/", corr_upper_lig)
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####################################################################
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####################################################################
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# end of loading libraries and functions #
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# end of loading libraries and functions #
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########################################################################
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########################################################################
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@ -159,8 +165,8 @@ my_corr_colnames = c("DUET"
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, "Foldx"
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, "Foldx"
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, "Log(OR)"
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, "Log (OR)"
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, "-Log(P)"
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, "-Log (P)"
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, "AF"
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, "AF"
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@ -173,9 +179,6 @@ colnames(corr_data_ps)
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colnames(corr_data_ps) <- my_corr_colnames
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colnames(corr_data_ps) <- my_corr_colnames
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colnames(corr_data_ps)
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colnames(corr_data_ps)
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#-----------------
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# generate corr PS plot
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#-----------------
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start = 1
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start = 1
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end = which(colnames(corr_data_ps) == drug); end # should be the last column
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end = which(colnames(corr_data_ps) == drug); end # should be the last column
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offset = 1
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offset = 1
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@ -187,11 +190,14 @@ head(my_corr_ps)
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# deep blue :#007d85
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# deep blue :#007d85
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# deep red: #ae301e
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# deep red: #ae301e
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#---------------------------------------
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# generate corr PS plot 1: both panels
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#---------------------------------------
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cat("Corr plot PS:", plot_corr_ps)
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cat("Corr plot PS:", plot_corr_ps)
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svg(plot_corr_ps, width = 15, height = 15)
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svg(plot_corr_ps, width = 15, height = 15)
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#OutPlot1 = pairs.panels([1:(length(my_corr_ps)-1)]
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OutPlot1 = pairs.panels(my_corr_ps[1:(length(my_corr_ps)-1)]
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OutPlot1 = my_pp(my_corr_ps[1:(length(my_corr_ps)-1)]
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, method = "spearman" # correlation method
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, method = "spearman" # correlation method
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, hist.col = "grey" ##00AFBB
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, hist.col = "grey" ##00AFBB
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, density = TRUE # show density plots
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, density = TRUE # show density plots
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@ -206,8 +212,8 @@ OutPlot1 = my_pp(my_corr_ps[1:(length(my_corr_ps)-1)]
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#, alpha = .05
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#, alpha = .05
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#, points(pch = 19, col = c("#f8766d", "#00bfc4"))
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#, points(pch = 19, col = c("#f8766d", "#00bfc4"))
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, cex = 3
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, cex = 3
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, cex.axis = 1.5
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, cex.axis = 2
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, cex.labels = 2.1
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, cex.labels = 4
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, cex.cor = 1
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, cex.cor = 1
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, smooth = F
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, smooth = F
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@ -216,6 +222,39 @@ OutPlot1 = my_pp(my_corr_ps[1:(length(my_corr_ps)-1)]
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print(OutPlot1)
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print(OutPlot1)
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dev.off()
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dev.off()
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#----------------------------------------------
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# generate corr PS plot 2: upper_panel only
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#----------------------------------------------
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cat("Corr plot upper PS:", plot_corr_upper_ps)
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svg(plot_corr_upper_ps, width = 15, height = 15)
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OutPlot1_upper = my_pp(my_corr_ps[1:(length(my_corr_ps)-1)] # no lower panel
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, method = "spearman" # correlation method
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, hist.col = "grey" ##00AFBB
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, density = TRUE # show density plots
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, ellipses = F # show correlation ellipses
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, stars = T
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, rug = F
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, breaks = "Sturges"
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, show.points = T
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, bg = c("#f8766d", "#00bfc4")[unclass(factor(my_corr_ps$duet_outcome))]
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, pch = 21
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, jitter = T
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#, alpha = .05
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#, points(pch = 19, col = c("#f8766d", "#00bfc4"))
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, cex = 3
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, cex.axis = 1.6
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, cex.labels = 4
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, cex.cor = 1
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, smooth = F
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)
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print(OutPlot1_upper)
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dev.off()
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################################################################################################
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#===========================
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#===========================
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# Data for Correlation plots: LIG
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# Data for Correlation plots: LIG
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#===========================
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#===========================
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@ -224,11 +263,9 @@ table(df_lig$ligand_outcome)
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df_lig$log10_or_mychisq = log10(df_lig$or_mychisq)
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df_lig$log10_or_mychisq = log10(df_lig$or_mychisq)
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df_lig$neglog_pval_fisher = -log10(df_lig$pval_fisher)
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df_lig$neglog_pval_fisher = -log10(df_lig$pval_fisher)
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df_lig$log10_or_kin = log10(df_lig$or_kin)
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df_lig$log10_or_kin = log10(df_lig$or_kin)
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df_lig$neglog_pwald_kin = -log10(df_lig$pwald_kin)
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df_lig$neglog_pwald_kin = -log10(df_lig$pwald_kin)
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# subset data to generate pairwise correlations
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# subset data to generate pairwise correlations
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cols_to_select = c("affinity_scaled"
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cols_to_select = c("affinity_scaled"
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@ -248,8 +285,8 @@ dim(corr_data_lig)
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# assign nice colnames (for display)
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# assign nice colnames (for display)
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my_corr_colnames = c("Ligand Affinity"
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my_corr_colnames = c("Ligand Affinity"
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, "Log(OR)"
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, "Log (OR)"
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, "-Log(P)"
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, "-Log (P)"
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, "AF"
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, "AF"
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@ -262,10 +299,6 @@ colnames(corr_data_lig)
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colnames(corr_data_lig) <- my_corr_colnames
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colnames(corr_data_lig) <- my_corr_colnames
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colnames(corr_data_lig)
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colnames(corr_data_lig)
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#-----------------
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# generate corr LIG plot
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#-----------------
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start = 1
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start = 1
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end = which(colnames(corr_data_lig) == drug); end # should be the last column
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end = which(colnames(corr_data_lig) == drug); end # should be the last column
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offset = 1
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offset = 1
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@ -273,32 +306,66 @@ offset = 1
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my_corr_lig = corr_data_lig[start:(end-offset)]
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my_corr_lig = corr_data_lig[start:(end-offset)]
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head(my_corr_lig)
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head(my_corr_lig)
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#---------------------------------------
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# generate corr LIG plot 1: both panels
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#---------------------------------------
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cat("Corr LIG plot:", plot_corr_lig)
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cat("Corr LIG plot:", plot_corr_lig)
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svg(plot_corr_lig, width = 15, height = 15)
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svg(plot_corr_lig, width = 15, height = 15)
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#OutPlot2 = pairs.panels(my_corr_lig[1:(length(my_corr_lig)-1)]
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# uncomment as necessary
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OutPlot2 = my_pp(my_corr_lig[1:(length(my_corr_lig)-1)]
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OutPlot2 = pairs.panels(my_corr_lig[1:(length(my_corr_lig)-1)]
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, method = "spearman" # correlation method
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, method = "spearman" # correlation method
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, hist.col = "grey" ##00AFBB
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, hist.col = "grey" ##00AFBB
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, density = TRUE # show density plots
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, density = TRUE # show density plots
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, ellipses = F # show correlation ellipses
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, ellipses = F # show correlation ellipses
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, stars = T
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, stars = T
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, rug = F
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, rug = F
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, breaks = "Sturges"
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, breaks = "Sturges"
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, show.points = T
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, show.points = T
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, bg = c("#f8766d", "#00bfc4")[unclass(factor(my_corr_lig$ligand_outcome))]
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, bg = c("#f8766d", "#00bfc4")[unclass(factor(my_corr_lig$ligand_outcome))]
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, pch = 21
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, pch = 21
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, jitter = T
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, jitter = T
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#, alpha = .05
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#, alpha = .05
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#, points(pch = 19, col = c("#f8766d", "#00bfc4"))
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#, points(pch = 19, col = c("#f8766d", "#00bfc4"))
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, cex = 3
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, cex = 3
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, cex.axis = 1.5
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, cex.axis = 2
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, cex.labels = 2.1
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, cex.labels = 4
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, cex.cor = 1
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, cex.cor = 1
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, smooth = F
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, smooth = F
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)
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)
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print(OutPlot2)
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print(OutPlot2)
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dev.off()
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dev.off()
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#---------------------------------------
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# generate corr LIG plot 2: upper panels
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#---------------------------------------
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cat("Corr LIG plot:", plot_corr_upper_lig)
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svg(plot_corr_upper_lig, width = 15, height = 15)
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# uncomment as necessary
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OutPlot2_upper = my_pp(my_corr_lig[1:(length(my_corr_lig)-1)]
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, method = "spearman" # correlation method
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, hist.col = "grey" ##00AFBB
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, density = TRUE # show density plots
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, ellipses = F # show correlation ellipses
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, stars = T
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, rug = F
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, breaks = "Sturges"
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, show.points = T
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, bg = c("#f8766d", "#00bfc4")[unclass(factor(my_corr_lig$ligand_outcome))]
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, pch = 21
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, jitter = T
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#, alpha = .05
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#, points(pch = 19, col = c("#f8766d", "#00bfc4"))
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, cex = 3
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, cex.axis = 1.6
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, cex.labels = 4
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, cex.cor = 1
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, smooth = F
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)
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print(OutPlot2_upper)
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dev.off()
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#######################################################
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#######################################################
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library(lattice)
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