added delta symbol to plotting_data.R and pretty labels for dr_other_muts figure
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3 changed files with 108 additions and 83 deletions
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@ -32,12 +32,13 @@ plot_point_legend = paste0(plotdir,"/", point_legend)
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#my_comparisons <- list( c(dr_muts_col, other_muts_col) )
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my_comparisons <- list( c("DM", "OM") )
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my_ats = 15# axis text size
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my_ats = 22# axis text size
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my_als = 20 # axis label size
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my_fls = 20 # facet label size
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my_pts = 22 # plot title size
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##########################################################################
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#===========
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# Plot1: PS
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#===========
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@ -65,7 +66,8 @@ p1 = ggplot(df_lf_ps, aes(x = mutation_info
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, vjust = 0)
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, axis.title.x = element_text(size = my_ats)
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, axis.title.y = element_text(size = my_ats)
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, plot.title = element_text(size = my_pts , hjust = 0.5)
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, plot.title = element_text(size = my_pts , hjust = 0.5, colour = "black", face = "bold")
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, strip.background = element_rect(fill = "khaki2")
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, strip.text.x = element_text(size = my_fls, colour = "black")
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, legend.title = element_text(color = "black", size = my_als)
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, legend.text = element_text(size = my_ats)
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@ -79,17 +81,65 @@ p1 = ggplot(df_lf_ps, aes(x = mutation_info
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#, label = "p.format")
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, label = "p.signif")
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p1
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#===============================================================
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#===========
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# Plot 2: LIG
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#===========
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##########################################################################
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#=================
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# Plot 2: Foldx
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#=================
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my_stat_foldx = compare_means(param_value~mutation_info, group.by = "param_type"
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, data = df_lf_foldx, paired = FALSE, p.adjust.method = "BH")
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y_value = "param_value"
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p2 = ggplot(df_lf_foldx, aes(x = mutation_info
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, y = eval(parse(text=y_value)) )) +
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facet_wrap(~ param_type
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, nrow = 1
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, scales = "free_y") +
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geom_boxplot(fill = "white", outlier.colour = NA
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#, position = position_dodge(width = 0.2)
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, width = 0.5) +
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geom_point(position = position_jitterdodge(dodge.width=0.01)
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, alpha = 0.5
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, show.legend = FALSE
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, aes(colour = factor(foldx_outcome))) +
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theme(axis.text.x = element_text(size = my_ats)
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, axis.text.y = element_text(size = my_ats
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, angle = 0
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, hjust = 1
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, vjust = 0)
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, axis.title.x = element_text(size = my_ats)
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, axis.title.y = element_text(size = my_ats)
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, plot.title = element_text(size = my_pts , hjust = 0.5, colour = "black", face = "bold")
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, strip.background = element_rect(fill = "palegreen1")
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, strip.text.x = element_text(size = my_fls, colour = "black")
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, legend.title = element_text(color = "black", size = my_als)
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, legend.text = element_text(size = my_ats)
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#, legend.title = element_blank()
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, legend.direction = "vertical") +
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labs(title = "Foldx"
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, x = ""
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, y = "") +
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stat_compare_means(comparisons = my_comparisons
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, method = "wilcox.test"
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, paired = FALSE
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#, label = "p.format")
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, label = "p.signif")
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p2
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##########################################################################
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#==============
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# Plot 3: LIG
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#==============
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my_stat_lig = compare_means(param_value~mutation_info, group.by = "param_type"
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, data = df_lf_lig, paired = FALSE, p.adjust.method = "BH")
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y_value = "param_value"
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p2 = ggplot(df_lf_lig, aes(x = mutation_info
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p3 = ggplot(df_lf_lig, aes(x = mutation_info
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, y = eval(parse(text=y_value)) )) +
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facet_wrap(~ param_type
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, nrow = 1
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@ -108,7 +158,8 @@ p2 = ggplot(df_lf_lig, aes(x = mutation_info
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, vjust = 0)
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, axis.title.x = element_text(size = my_ats)
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, axis.title.y = element_text(size = my_ats)
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, plot.title = element_text(size = my_pts , hjust = 0.5)
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, plot.title = element_text(size = my_pts , hjust = 0.5, colour = "black", face = "bold")
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, strip.background = element_rect(fill = "thistle3")
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, strip.text.x = element_text(size = my_fls, colour = "black")
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, legend.title = element_text(color = "black", size = my_als)
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, legend.text = element_text(size = my_ats)
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@ -122,58 +173,12 @@ p2 = ggplot(df_lf_lig, aes(x = mutation_info
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#, label = "p.format")
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, label = "p.signif")
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p2
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p3
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#====================================================================
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#===========
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# Plot 3: Foldx
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#===========
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my_stat_foldx = compare_means(param_value~mutation_info, group.by = "param_type"
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, data = df_lf_foldx, paired = FALSE, p.adjust.method = "BH")
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y_value = "param_value"
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p3 = ggplot(df_lf_foldx, aes(x = mutation_info
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, y = eval(parse(text=y_value)) )) +
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facet_wrap(~ param_type
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, nrow = 1
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, scales = "free_y") +
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geom_boxplot(fill = "white", outlier.colour = NA
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#, position = position_dodge(width = 0.2)
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, width = 0.5) +
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geom_point(position = position_jitterdodge(dodge.width=0.01)
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, alpha = 0.5
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, show.legend = FALSE
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, aes(colour = factor(foldx_outcome))) +
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theme(axis.text.x = element_text(size = my_ats)
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, axis.text.y = element_text(size = my_ats
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, angle = 0
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, hjust = 1
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, vjust = 0)
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, axis.title.x = element_text(size = my_ats)
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, axis.title.y = element_text(size = my_ats)
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, plot.title = element_text(size = my_pts , hjust = 0.5)
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, strip.text.x = element_text(size = my_fls, colour = "black")
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#, legend.title = element_text(color = "black", size = my_als)
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, legend.text = element_text(size = my_ats)
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, legend.direction = "vertical"
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, legend.title = element_blank()) +
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labs(title = ""
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, x = ""
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, y = "") +
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stat_compare_means(comparisons = my_comparisons
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, method = "wilcox.test"
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, paired = FALSE
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#, label = "p.format")
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, label = "p.signif")
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p3
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#====================================================================
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##########################################################################
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#===========
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# legend
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#===========
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legend = ggplot(df_lf_foldx, aes(x = mutation_info
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, y = eval(parse(text=y_value)) )) +
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facet_wrap(~ param_type
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@ -186,12 +191,15 @@ legend = ggplot(df_lf_foldx, aes(x = mutation_info
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, aes(colour = factor(foldx_outcome))) +
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theme(legend.text = element_text(size = 25)
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, legend.direction = "vertical"
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, legend.title = element_blank())+
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, legend.title = element_blank()
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#, axis.text.y = element_text(size = 30, colour = "black", angle = 90)
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#, axis.text.x = element_text(size = 30, colour = "black", angle = 0)
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#, strip.background = element_rect(fill="orange")
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) +
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guides(color = guide_legend(override.aes = list(size = 6)))
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legend
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##########################################################################
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#===========================
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# combine
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#===========================
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@ -202,24 +210,19 @@ cat("Output plot:",plot_dr_other_combined)
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svg(plot_dr_other_combined, width = 24, height = 12)
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#theme_set(theme_gray()) # to preserve default theme
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OutPlot = cowplot::plot_grid(p1, p2
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, nrow = 2
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, align = "hv"
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, axis = "b"
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, labels = c("", "", "")
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, label_size = my_als)
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# first combine fold and lig plots (2 and 3)
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c1 = cowplot::plot_grid(p2, p3
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, nrow = 1
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, rel_widths = c(1/6, 5/6))
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c1
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OutPlot = cowplot::plot_grid(p1, c1
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, nrow = 2)
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print(OutPlot)
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dev.off()
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#---------
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# plot 2
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#---------
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svg(plot_dr_other_foldx , width = 6, height = 7)
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OutPlot2 = p3
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print(OutPlot2)
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dev.off()
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#---------
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# plot 3: legend
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#---------
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@ -227,3 +230,13 @@ svg(plot_point_legend, width = 6, height = 7)
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OutPlot3 = legend
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print(OutPlot3)
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dev.off()
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@ -110,14 +110,12 @@ df_lig = merged_df3_lig
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# name tidying
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df_lig$mutation_info = as.factor(df_lig$mutation_info)
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df_lig$duet_outcome = as.factor(df_lig$duet_outcome)
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df_lig$ligand_outcome = as.factor(df_lig$ligand_outcome)
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#df_lig$ligand_outcome = as.factor(df_lig$ligand_outcome)
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# check
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table(df_lig$mutation_info)
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#========================================================================
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#===========
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# Data: ps
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#===========
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@ -155,8 +153,16 @@ str(df_lf_ps)
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# assign pretty labels: param_type
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levels(df_lf_ps$param_type); table(df_lf_ps$param_type)
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levels(df_lf_ps$param_type)[levels(df_lf_ps$param_type)=="duet_scaled"] <- "DUET"
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levels(df_lf_ps$param_type)[levels(df_lf_ps$param_type)=="ligand_distance"] <- "Ligand Distance"
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ligand_dist_colname = paste0("Distance to ligand (", angstroms_symbol, ")")
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ligand_dist_colname
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duet_stability_name = paste0(delta_symbol, delta_symbol, "G")
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duet_stability_name
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#levels(df_lf_ps$param_type)[levels(df_lf_ps$param_type)=="duet_scaled"] <- "Stability"
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levels(df_lf_ps$param_type)[levels(df_lf_ps$param_type)=="duet_scaled"] <- duet_stability_name
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#levels(df_lf_ps$param_type)[levels(df_lf_ps$param_type)=="ligand_distance"] <- "Ligand Distance"
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levels(df_lf_ps$param_type)[levels(df_lf_ps$param_type)=="ligand_distance"] <- ligand_dist_colname
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levels(df_lf_ps$param_type)[levels(df_lf_ps$param_type)=="asa"] <- "ASA"
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levels(df_lf_ps$param_type)[levels(df_lf_ps$param_type)=="rsa"] <- "RSA"
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levels(df_lf_ps$param_type)[levels(df_lf_ps$param_type)=="rd_values"] <- "RD"
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@ -183,7 +189,7 @@ cols_to_select_lig = c("mutationinformation", "mutation", "position", "mutation_
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, "ligand_outcome"
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, "affinity_scaled"
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, "ligand_distance"
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#, "ligand_distance"
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, "asa"
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, "rsa"
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, "rd_values"
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@ -210,7 +216,7 @@ if (nrow(df_lf_lig) == expected_rows_lf_lig){
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levels(df_lf_lig$param_type); table(df_lf_lig$param_type)
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levels(df_lf_lig$param_type)[levels(df_lf_lig$param_type)=="affinity_scaled"] <- "Ligand Affinity"
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levels(df_lf_lig$param_type)[levels(df_lf_lig$param_type)=="ligand_distance"] <- "Ligand Distance"
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#levels(df_lf_lig$param_type)[levels(df_lf_lig$param_type)=="ligand_distance"] <- "Ligand Distance"
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levels(df_lf_lig$param_type)[levels(df_lf_lig$param_type)=="asa"] <- "ASA"
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levels(df_lf_lig$param_type)[levels(df_lf_lig$param_type)=="rsa"] <- "RSA"
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levels(df_lf_lig$param_type)[levels(df_lf_lig$param_type)=="rd_values"] <- "RD"
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@ -260,10 +266,14 @@ if (nrow(df_lf_foldx) == expected_rows_lf_foldx){
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exit()
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}
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foldx_stability_name = paste0(delta_symbol, delta_symbol, "G")
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foldx_stability_name
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# assign pretty labels: param type
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levels(df_lf_foldx$param_type); table(df_lf_foldx$param_type)
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levels(df_lf_foldx$param_type)[levels(df_lf_foldx$param_type)=="foldx_scaled"] <- "Foldx"
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#levels(df_lf_foldx$param_type)[levels(df_lf_foldx$param_type)=="foldx_scaled"] <- "Stability"
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levels(df_lf_foldx$param_type)[levels(df_lf_foldx$param_type)=="foldx_scaled"] <- foldx_stability_name
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#levels(df_lf_foldx$param_type)[levels(df_lf_foldx$param_type)=="ligand_distance"] <- "Ligand Distance"
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#levels(df_lf_foldx$param_type)[levels(df_lf_foldx$param_type)=="asa"] <- "ASA"
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#levels(df_lf_foldx$param_type)[levels(df_lf_foldx$param_type)=="rsa"] <- "RSA"
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@ -97,6 +97,8 @@ my_df_u_lig = my_df_u[my_df_u$ligand_distance <10,]
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angstroms_symbol = "\u212b"
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cat(paste0("There are ", nrow(my_df_u_lig), " sites lying within 10", angstroms_symbol, " of the ligand\n"))
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delta_symbol = "\u0394"; delta_symbol
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########################################################################
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# end of data extraction and cleaning for plots #
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########################################################################
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