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nearly, adding correct y_pos to plot the stat labels

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Tanushree Tunstall 2020-10-30 19:48:28 +00:00
parent af334b559e
commit 1ed09ac20b
1 changed files with 95 additions and 4 deletions
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99
boxplot_with_stats.R
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@ -9,8 +9,7 @@ getwd()
#=============
# Input
#=============
source("boxplot_linear.R")
#source("boxplot_linear.R")
#######################################################
med_names = c("eotaxin3", "il12p70", "itac", "il13")
lf_test = lf_fp_npa[lf_fp_npa$mediator%in%med_names,]
@ -38,7 +37,11 @@ p2 = ggplot(single)+ geom_boxplot(aes(x = timepoint
, axis.title.x = element_blank()
, axis.title.y = element_blank()
, legend.position = "none"
, plot.title = element_text(size = 20, hjust = 0.5))
, plot.subtitle = element_text(size = 20, hjust = 0.5)
, plot.title = element_text(size = 20, hjust = 0.5)) +
labs(title = i
#, subtitle = "test2"
)
stat_npa2 <- single %>%
group_by(timepoint, mediator) %>%
@ -50,7 +53,7 @@ stat_npa2 <- stat_npa2 %>%
add_xy_position(x = "timepoint", dodge = 0.8)
p2 = p2 + stat_pvalue_manual(stat_npa2
, y.position = max_y
#, y.position = max_y
, label = "{p} {p.signif}"
, hide.ns=T
, tip.length = 0)+
@ -59,3 +62,91 @@ plots[[i]] <- p2
}
cowplot::plot_grid(plotlist=plots, align = 'hv', ncol=2, nrow=2)
##################################################################
#=======
# facet
#=======
#--------
# wilcox stats
#--------
stat_npa3 <- lf_test %>%
group_by(timepoint, mediator) %>%
wilcox_test(value ~ obesity, paired = F) %>%
add_significance("p")
stat_npa3
stat_npa3 <- stat_npa3 %>%
add_xy_position(x = "timepoint", dodge = 0.8)
head(stat_npa3)
#--------
# summary stats
#--------
my_summary = lf_test %>%
group_by(timepoint, mediator) %>%
get_summary_stats(value)
my_summary
my_max_df = subset(my_summary
, select = c("mediator", "timepoint"
#, "obesity"
, "max"))
head(my_max_df); head(stat_npa3)
#-----------------------------
# merge my_max and stat_npa3
#-----------------------------
head(my_max_df)
merging_cols = intersect(names(stat_npa3), names(my_max_df)); merging_cols
stat_npa3_v2 = merge(stat_npa3, my_max_df, by = merging_cols, all.x = T)
stat_npa3_v2$my_y_pos = (stat_npa3_v2$max)*1.2
stat_npa3_v2$my_y_pos
head(stat_npa3_v2); head(stat_npa3)
p3 = ggplot(lf_test)+ geom_boxplot(aes(x = timepoint
, y = value
, color = obesity))+
theme(axis.text.x = element_text(size = 15)
, axis.text.y = element_text(size = 15
, angle = 0
, hjust = 1
, vjust = 0)
, axis.title.x = element_blank()
, axis.title.y = element_blank()
, legend.position = "none"
, plot.subtitle = element_text(size = 20, hjust = 0.5)
, plot.title = element_text(size = 20, hjust = 0.5)) +
labs(title ="NPA")+
#facet_wrap(~mediator, scales = "free")
p3_build = ggbuild(p3)
p4 = p3 + stat_pvalue_manual(stat_npa3_v2
, y.position = "my_y_pos"
#, y.position = 50
, label = "{p} {p.signif}"
, hide.ns=T
, tip.length = 0)+
scale_y_continuous(expand = expansion(mult = c(0.05, 0.25)))
p4
#========================================
p3_build = ggplot_build(p3)
p3_build$layout$panel_scales_y
get_facet_ymax <- function (x){
ret <- x$layout$panel_scales_y
y_max = NULL
for (i in 1:length(ret)){
print(i)
y_max_i <- max(x$layout$panel_scales_y[[i]]$range$range)
y_max = c(y_max, y_max_i)
}
return(y_max)
}
y_max_l = get_facet_ymax(p3_build); y_max_l