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added functions for bp with stat and tested them

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Tanushree Tunstall 2021-08-27 14:05:00 +01:00
parent edb409baef
commit 826d3c72b7
4 changed files with 103 additions and 105 deletions
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scripts/functions/lf_bp_with_stats.R Normal file
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library(ggpubr)
###################################################################
####################################
lf_bp_with_stats <- function(lf_df
, x_grp = "mutation_info"
, y_var = "param_value"
, facet_var = "param_type"
, n_facet_row = 1
, y_scales = "free_y"
, p_title = ""
, colour_categ = ""
, colour_bp_strip = "khaki2"
, stat_grp_comp = c("DM", "OM")
, stat_method = "wilcox.test"
, my_paired = FALSE
#, stat_label = "p.format")
, stat_label = c("p.format", "p.signif")
, my_ats = 22 # axis text size
, my_als = 20 # axis label size
, my_fls = 20 # facet label size
, my_pts = 22 # plot title size
) {
my_comparisonsL <- list( stat_grp_comp )
bp_statP <- ggplot(lf_df, aes(x = eval(parse(text = x_grp))
, y = eval(parse(text = y_var)) )) +
facet_wrap(~ eval(parse(text = facet_var))
, nrow = n_facet_row
, scales = y_scales) +
geom_boxplot(fill = "white", outlier.colour = NA
#, position = position_dodge(width = 0.9)
, width = 0.2) +
geom_point(position = position_jitterdodge(dodge.width = 0.01)
, alpha = 0.5
, show.legend = FALSE
, aes(colour = factor(eval(parse(text = colour_categ))) )) +
theme(axis.text.x = element_text(size = my_ats)
, axis.text.y = element_text(size = my_ats
, angle = 0
, hjust = 1
, vjust = 0)
, axis.title.x = element_text(size = my_ats)
, axis.title.y = element_text(size = my_ats)
, plot.title = element_text(size = my_pts , hjust = 0.5, colour = "black", face = "bold")
, strip.background = element_rect(fill = colour_bp_strip)
, strip.text.x = element_text(size = my_fls, colour = "black")
, legend.title = element_text(color = "black", size = my_als)
, legend.text = element_text(size = my_ats)
, legend.direction = "vertical") +
labs(title = p_title
, x = ""
, y = "")+
stat_compare_means(comparisons = my_comparisonsL
, method = stat_method
, paired = my_paired
#, label = "p.format")
, label = stat_label[1])
return(bp_statP)
}