added boxplots and stats for other numerical params
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scripts/plotting/other_plots.R
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173
scripts/plotting/other_plots.R
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#!/usr/bin/env Rscript
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#########################################################
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# TASK: producing boxplots for dr and other muts
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#########################################################
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#=======================================================================
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# working dir and loading libraries
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getwd()
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setwd("~/git/LSHTM_analysis/scripts/plotting")
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getwd()
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source("Header_TT.R")
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#library(ggplot2)
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#library(data.table)
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#library(dplyr)
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source("other_plots_data.R")
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#=======
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# output
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#=======
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#dr_other_plots_combined = "dr_other_combined.svg"
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#plot_dr_other_plots_combined = paste0(plotdir,"/", dr_other_plots_combined)
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########################################################################
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# end of data extraction and cleaning for plots #
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########################################################################
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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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#===========
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# Plot1: PS
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#===========
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my_stat_ps = compare_means(param_value~mutation_info, group.by = "param_type"
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, data = df_lf_ps, paired = FALSE, p.adjust.method = "BH")
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y_value = "param_value"
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p1 = ggplot(df_lf_ps, 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 = 0.9)
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, width = 0.5) +
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geom_point(position = position_jitterdodge(dodge.width=0.01)
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, show.legend = FALSE
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, aes(colour = factor(duet_outcome))) +
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theme(axis.text.x = element_text(size = 15)
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, axis.text.y = element_text(size = 15
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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 = 15)
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, axis.title.y = element_text(size = 15)
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, plot.title = element_text(size = 20, hjust = 0.5)
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, strip.text.x = element_text(size = 15, colour = "black")
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, legend.title = element_text(color = "black", size = 20)
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, legend.text = element_text(size = 15)
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, legend.direction = "vertical") +
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labs(title = "DUET"
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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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p1
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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 = 0.9)
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, width = 0.5) +
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geom_point(position = position_jitterdodge(dodge.width=0.01)
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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 = 15)
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, axis.text.y = element_text(size = 15
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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 = 15)
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, axis.title.y = element_text(size = 15)
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, plot.title = element_text(size = 20, hjust = 0.5)
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, strip.text.x = element_text(size = 15, colour = "black")
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, legend.title = element_text(color = "black", size = 20)
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, legend.text = element_text(size = 15)
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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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# 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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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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, scales = "free_y") +
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geom_boxplot(fill = "white", outlier.colour = NA
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# position = position_dodge(width = 0.9)
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, width = 0.5) +
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geom_point(position = position_jitterdodge(dodge.width=0.01)
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, show.legend = FALSE
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, aes(colour = factor(ligand_outcome))) +
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theme(axis.text.x = element_text(size = 15)
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, axis.text.y = element_text(size = 15
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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 = 15)
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, axis.title.y = element_text(size = 15)
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, plot.title = element_text(size = 20, hjust = 0.5)
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, strip.text.x = element_text(size = 15, colour = "black")
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, legend.title = element_text(color = "black", size = 20)
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, legend.text = element_text(size = 15)
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, legend.direction = "vertical") +
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labs(title = "Ligand Affinity"
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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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# combine
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#===========================
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#svg(plot_or_combined, width = 32, height = 12)
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theme_set(theme_gray()) # to preserve default theme
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printFile = cowplot::plot_grid(plot_grid(p1, p2, p3
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, nrow = 3
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, align = 'h'
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, labels = c("", "", "")
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, label_size = 20))
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print(printFile)
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dev.off()
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