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fixed colours as well

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This commit is contained in:
Tanushree Tunstall 2020-10-30 20:56:15 +00:00
parent 1ed09ac20b
commit 8015dd4d6a
1 changed files with 92 additions and 9 deletions
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101
boxplot_with_stats.R
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@ -9,7 +9,7 @@ getwd()
#============= #=============
# Input # Input
#============= #=============
#source("boxplot_linear.R") source("boxplot_linear.R")
####################################################### #######################################################
med_names = c("eotaxin3", "il12p70", "itac", "il13") med_names = c("eotaxin3", "il12p70", "itac", "il13")
lf_test = lf_fp_npa[lf_fp_npa$mediator%in%med_names,] lf_test = lf_fp_npa[lf_fp_npa$mediator%in%med_names,]
@ -73,7 +73,8 @@ stat_npa3 <- lf_test %>%
group_by(timepoint, mediator) %>% group_by(timepoint, mediator) %>%
wilcox_test(value ~ obesity, paired = F) %>% wilcox_test(value ~ obesity, paired = F) %>%
add_significance("p") add_significance("p")
stat_npa3 stat_npa3
stat_npa3$p_format = round(stat_npa3$p, 3)
stat_npa3 <- stat_npa3 %>% stat_npa3 <- stat_npa3 %>%
add_xy_position(x = "timepoint", dodge = 0.8) add_xy_position(x = "timepoint", dodge = 0.8)
@ -108,6 +109,8 @@ head(stat_npa3_v2); head(stat_npa3)
p3 = ggplot(lf_test)+ geom_boxplot(aes(x = timepoint p3 = ggplot(lf_test)+ geom_boxplot(aes(x = timepoint
, y = value , y = value
, color = obesity))+ , color = obesity))+
scale_colour_manual(values=c("blue", "red")) +
theme(axis.text.x = element_text(size = 15) theme(axis.text.x = element_text(size = 15)
, axis.text.y = element_text(size = 15 , axis.text.y = element_text(size = 15
, angle = 0 , angle = 0
@ -115,24 +118,25 @@ p3 = ggplot(lf_test)+ geom_boxplot(aes(x = timepoint
, vjust = 0) , vjust = 0)
, axis.title.x = element_blank() , axis.title.x = element_blank()
, axis.title.y = element_blank() , axis.title.y = element_blank()
, legend.position = "none" , strip.text.x = element_text(size = 20)
, legend.position = "top"
, legend.title = element_text(color = "black", size = 20)
, legend.text = element_text(size = 15)
, plot.subtitle = 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)) + , plot.title = element_text(size = 20, hjust = 0.5)) +
labs(title ="NPA")+ labs(title ="NPA")+
#facet_wrap(~mediator, scales = "free") facet_wrap(~mediator, scales = "free", nrow = 2, ncol = 2)
#p3
p3_build = ggbuild(p3)
p4 = p3 + stat_pvalue_manual(stat_npa3_v2 p4 = p3 + stat_pvalue_manual(stat_npa3_v2
, y.position = "my_y_pos" , y.position = "my_y_pos"
#, y.position = 50 #, y.position = 50
, label = "{p} {p.signif}" , label = "{p_format} {p.signif}"
, hide.ns=T , hide.ns=T
, tip.length = 0)+ , tip.length = 0)+
scale_y_continuous(expand = expansion(mult = c(0.05, 0.25))) scale_y_continuous(expand = expansion(mult = c(0.05, 0.25)))
p4 p4
#======================================== #=======================================
p3_build = ggplot_build(p3) p3_build = ggplot_build(p3)
p3_build$layout$panel_scales_y p3_build$layout$panel_scales_y
@ -150,3 +154,82 @@ get_facet_ymax <- function (x){
} }
y_max_l = get_facet_ymax(p3_build); y_max_l y_max_l = get_facet_ymax(p3_build); y_max_l
#===============================================
# facet wrap on actual data
pdf("boxplot_stats.pdf", width = 20, height = 15)
#=======
# facet
#=======
#--------
# wilcox stats
#--------
stat_npa3 <- lf_fp_npa %>%
group_by(timepoint, mediator) %>%
wilcox_test(value ~ obesity, paired = F) %>%
add_significance("p")
stat_npa3
stat_npa3$p_format = round(stat_npa3$p, 3)
stat_npa3 <- stat_npa3 %>%
add_xy_position(x = "timepoint", dodge = 0.8)
head(stat_npa3)
#--------
# summary stats
#--------
my_summary = lf_fp_npa %>%
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_fp_npa)+ geom_boxplot(aes(x = timepoint
, y = value
, color = obesity))+
scale_colour_manual(values=c("blue", "red")) +
scale_y_log10()+
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()
, strip.text.x = element_text(size = 20)
, legend.position = "top"
, legend.title = element_text(color = "black", size = 20)
, legend.text = element_text(size = 15)
, 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", nrow = 5, ncol = 7)
#p3
p4 = p3 + stat_pvalue_manual(stat_npa3_v2
, y.position = "my_y_pos"
#, y.position = 50
, label = "{p_format} {p.signif}"
, hide.ns=T
, tip.length = 0) #+
#scale_y_continuous(expand = expansion(mult = c(0.05, 0.25)))
p4
dev.off()