tanu/mosaic_2020
1
0
Fork 0
Code Issues Pull requests Releases Wiki Activity

tweaking layout in test

Browse source
This commit is contained in:
Tanushree Tunstall 2020-10-31 18:30:20 +00:00
parent 8015dd4d6a
commit 558f57c61e
1 changed files with 12 additions and 8 deletions
Download patch file Download diff file Expand all files Collapse all files

20
boxplot_with_stats.R
View file

@ -15,6 +15,8 @@ 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,]
mediators = levels(as.factor(lf_test$mediator)) mediators = levels(as.factor(lf_test$mediator))
mediators = levels(as.factor(lf_fp_npa$mediator))
lf_test = lf_fp_npa
plots <- list() plots <- list()
@ -29,6 +31,7 @@ p2 = ggplot(single)+ geom_boxplot(aes(x = timepoint
, color = obesity , color = obesity
#, palette = c("#00BFC4", "#F8766D") #, palette = c("#00BFC4", "#F8766D")
))+ ))+
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
@ -62,6 +65,9 @@ plots[[i]] <- p2
} }
cowplot::plot_grid(plotlist=plots, align = 'hv', ncol=2, nrow=2) cowplot::plot_grid(plotlist=plots, align = 'hv', ncol=2, nrow=2)
pdf("test.pdf", width = 22, height = 16)
cowplot::plot_grid(plotlist=plots, align = 'hv', ncol=7, nrow=5)
dev.off()
################################################################## ##################################################################
#======= #=======
# facet # facet
@ -118,7 +124,7 @@ 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()
, strip.text.x = element_text(size = 20) , strip.text.x = element_text(size = 20,margin = margin(0.05,0,0.07,0, "cm"))
, legend.position = "top" , legend.position = "top"
, legend.title = element_text(color = "black", size = 20) , legend.title = element_text(color = "black", size = 20)
, legend.text = element_text(size = 15) , legend.text = element_text(size = 15)
@ -182,9 +188,7 @@ my_summary = lf_fp_npa %>%
get_summary_stats(value) get_summary_stats(value)
my_summary my_summary
my_max_df = subset(my_summary my_max_df = subset(my_summary
, select = c("mediator", "timepoint" , select = c("mediator", "timepoint", "max"))
#, "obesity"
, "max"))
head(my_max_df); head(stat_npa3) head(my_max_df); head(stat_npa3)
@ -205,8 +209,7 @@ p3 = ggplot(lf_fp_npa)+ geom_boxplot(aes(x = timepoint
, y = value , y = value
, color = obesity))+ , color = obesity))+
scale_colour_manual(values=c("blue", "red")) + scale_colour_manual(values=c("blue", "red")) +
scale_y_log10()+ #scale_y_log10()+
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
@ -214,7 +217,7 @@ p3 = ggplot(lf_fp_npa)+ 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()
, strip.text.x = element_text(size = 20) , strip.text.x = element_text(size = 20, margin = margin(2,0,2,0, "cm"))
, legend.position = "top" , legend.position = "top"
, legend.title = element_text(color = "black", size = 20) , legend.title = element_text(color = "black", size = 20)
, legend.text = element_text(size = 15) , legend.text = element_text(size = 15)
@ -225,6 +228,7 @@ p3 = ggplot(lf_fp_npa)+ geom_boxplot(aes(x = timepoint
#p3 #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"
, step.increase = 0.08
#, y.position = 50 #, y.position = 50
, label = "{p_format} {p.signif}" , label = "{p_format} {p.signif}"
, hide.ns=T , hide.ns=T
@ -232,4 +236,4 @@ p4 = p3 + stat_pvalue_manual(stat_npa3_v2
#scale_y_continuous(expand = expansion(mult = c(0.05, 0.25))) #scale_y_continuous(expand = expansion(mult = c(0.05, 0.25)))
p4 p4
dev.off() dev.off()