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renamed dm_om barplot function scriptto lf_bp_stability.R

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Tanushree Tunstall 2021-08-27 13:03:39 +01:00
parent 14d1ec84ab
commit 873049b603
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100
scripts/functions/stat_bp_stability.R
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@ -1,100 +0,0 @@
library(ggpubr)
###################################################################
my_unpaired_stats <- function(lf_data
, lf_stat_value = "param_value"
, lf_stat_group = "mutation_info"
, lf_col_statvars = "param_type"
, my_paired = FALSE
, stat_adj = "none"){
stat_formula = as.formula(paste0(lf_stat_value, "~", lf_stat_group))
my_stat_df = compare_means(stat_formula
, group.by = lf_col_statvars
, data = lf_data
, paired = my_paired
, p.adjust.method = stat_adj)
return(my_stat_df)
}
#####################
# call stat function
#####################
stat_results_df <- my_unpaired_stats(lf_data = lf_duet
, lf_stat_value = "param_value"
, lf_stat_group = "mutation_info"
, lf_col_statvars = "param_type"
, my_paired = FALSE
, stat_adj = "none"
)
y_value = "param_value"
#################################
my_comparisons <- list( c("DM", "OM") )
my_ats = 22 # axis text size
my_als = 20 # axis label size
my_fls = 20 # facet label size
my_pts = 22 # plot title size
####################################
stat_bp_mut <- function(df
, x_bp_cateog = "mutation_info"
, y_var = "param_value"
, facet_var = "param_type"
, scales = "free_y"
, title = ""
, col_categ = "duet_outcome"
, grp_comp = "my_comparisons"
, stat_method = "wilcox.test"
, my_paired = FALSE
#, stat_label = "p.format")
, stat_label = "p.signif" )
#############################
y_value = "param_value"
p1 = ggplot(lf_duet, aes(x = mutation_info
, y = eval(parse(text = y_value)) )) +
facet_wrap(~ param_type
, nrow = 1
, scales = "free_y") +
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(duet_outcome))) +
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 = "khaki2")
, 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 = "DUET"
, x = ""
, y = "")+
stat_compare_means(comparisons = my_comparisons
, method = "wilcox.test"
, paired = FALSE
#, label = "p.format")
, label = "p.signif")
p1