added functions for bp with stat and tested them
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4 changed files with 103 additions and 105 deletions
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library(ggpubr)
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###################################################################
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my_unpaired_stats <- function(lf_data
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, lf_stat_value = "param_value"
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, lf_stat_group = "mutation_info"
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, lf_col_statvars = "param_type"
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, my_paired = FALSE
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, stat_adj = "none"){
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stat_formula = as.formula(paste0(lf_stat_value, "~", lf_stat_group))
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my_stat_df = compare_means(stat_formula
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, group.by = lf_col_statvars
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, data = lf_data
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, paired = my_paired
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, p.adjust.method = stat_adj)
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return(my_stat_df)
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}
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#####################
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# call stat function
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#####################
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stat_results_df <- my_unpaired_stats(lf_data = lf_duet
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, lf_stat_value = "param_value"
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, lf_stat_group = "mutation_info"
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, lf_col_statvars = "param_type"
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, my_paired = FALSE
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, stat_adj = "none"
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)
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y_value = "param_value"
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#################################
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my_comparisons <- list( c("DM", "OM") )
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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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stat_bp_mut <- function(df
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, x_bp_cateog = "mutation_info"
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, y_var = "param_value"
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, facet_var = "param_type"
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, scales = "free_y"
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, title = ""
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, col_categ = "duet_outcome"
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, grp_comp = "my_comparisons"
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, stat_method = "wilcox.test"
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, my_paired = FALSE
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#, stat_label = "p.format")
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, stat_label = "p.signif" )
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#############################
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y_value = "param_value"
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p1 = ggplot(lf_duet, 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 = 0.2) +
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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(duet_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 = "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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, 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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68
scripts/functions/lf_bp_with_stats.R
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68
scripts/functions/lf_bp_with_stats.R
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library(ggpubr)
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###################################################################
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####################################
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lf_bp_with_stats <- function(lf_df
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, x_grp = "mutation_info"
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, y_var = "param_value"
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, facet_var = "param_type"
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, n_facet_row = 1
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, y_scales = "free_y"
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, p_title = ""
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, colour_categ = ""
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, colour_bp_strip = "khaki2"
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, stat_grp_comp = c("DM", "OM")
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, stat_method = "wilcox.test"
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, my_paired = FALSE
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#, stat_label = "p.format")
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, stat_label = c("p.format", "p.signif")
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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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my_comparisonsL <- list( stat_grp_comp )
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bp_statP <- ggplot(lf_df, aes(x = eval(parse(text = x_grp))
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, y = eval(parse(text = y_var)) )) +
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facet_wrap(~ eval(parse(text = facet_var))
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, nrow = n_facet_row
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, scales = y_scales) +
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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 = 0.2) +
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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(eval(parse(text = colour_categ))) )) +
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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 = colour_bp_strip)
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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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labs(title = p_title
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, x = ""
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, y = "")+
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stat_compare_means(comparisons = my_comparisonsL
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, method = stat_method
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, paired = my_paired
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#, label = "p.format")
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, label = stat_label[1])
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return(bp_statP)
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}
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28
scripts/functions/test_lf_bp_with_stats.R
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28
scripts/functions/test_lf_bp_with_stats.R
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setwd("~/git/LSHTM_analysis/scripts/plotting/")
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source("../functions/lf_bp_with_stats.R")
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######################
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# call function
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######################
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# Note: Data
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# run other_plots_data.R
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# to get the long format data to test this function
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lf_bp_with_stats(lf_df = lf_dynamut2
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, x_grp = "mutation_info"
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, y_var = "param_value"
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, facet_var = "param_type"
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, n_facet_row = 1
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, y_scales = "free_y"
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, p_title = "Dynamut2"
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, colour_categ = "ddg_dynamut2_outcome"
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, stat_grp_comp = c("DM", "OM")
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, stat_method = "wilcox.test"
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, my_paired = FALSE
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#, stat_label = "p.format")
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, stat_label = c("p.format", "p.signif")
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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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@ -1,13 +1,15 @@
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setwd("~/git/LSHTM_analysis/scripts/functions")
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source("lf_unpaired_stats.R")
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#####################
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# call stat function()
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# a useful way to check stats
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# for any lf data
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#####################
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# Note: Data
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# run other_plots_data.R
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# to get the df you want to test this function
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# to get the long format data to test this function
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#####################
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# call stat function
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#####################
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stat_results_df <- lf_unpaired_stats(lf_data = lf_duet
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, lf_stat_value = "param_value"
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, lf_stat_group = "mutation_info"
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