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

playing with display

Browse source
This commit is contained in:
Tanushree Tunstall 2020-10-29 17:41:39 +00:00
parent 2634aeeb84
commit c26171d12c
1 changed files with 52 additions and 41 deletions
Download patch file Download diff file Expand all files Collapse all files

93
boxplot.R
View file

@ -78,11 +78,6 @@ stat.test <- stat.test %>%
bxp + stat_pvalue_manual(
stat.test, label = "p", tip.length = 0
)
################################
lf_test2 = lf[order(lf$mediator),] # 2 meds
lf_test2 = lf_test2[1:798,]
@ -98,7 +93,6 @@ stat.test <- lf_test2 %>%
stat.test
bxp <- ggboxplot(lf_test2, x = "timepoint", y = "value",
color = "obesity", palette = c("#00BFC4", "#F8766D")) +
facet_wrap(~mediator, scales = "free_y")
@ -116,45 +110,62 @@ str(lf_comp)
p2 = ggplot(lf_test_comp, aes(x = timepoint, y = value, fill = obesity )) +
geom_boxplot(width = 0.5)
p2 + stat_compare_means(comparisons = my_comparisons
, method = "wilcox.test"
, paired = F
, label = "p.format")
p2
########################################################################
# Output plots as one pdf
cat("Output plots will be in:", output_boxplot)
pdf(output_boxplot, width=15, height=12)
pdf(output_boxplot, width = 25, height = 15)
y_value = "value"
my_title1 = "Boxplots"
#stats data
str(lf)
stat.test <- lf %>%
group_by(timepoint, mediator) %>%
wilcox_test(value ~ obesity, paired = F) %>%
#adjust_pvalue(method = "bonferroni") %>%
#add_significance("p.adj")
add_significance("p")
stat.test
bxp <- ggboxplot(lf, x = "timepoint", y = "value",
color = "obesity", palette = c("#00BFC4", "#F8766D")) +
facet_wrap(~mediator, nrow = 7, ncol = 5, scales = "free_y", shrink = T)+
scale_y_log10()
bxp
bxp + stat.test <- stat.test %>%
add_xy_position(x = "timepoint", dodge = 0.8)
bxp + stat_pvalue_manual(stat.test, label = "p.signif", tip.length = 0)
p1 = ggplot(lf, aes(x = factor(timepoint), y = eval(parse(text=y_value)), fill = factor(obesity) )) +
scale_fill_manual(values=c("#00BFC4", "#F8766D")) +
facet_wrap(~ mediator, nrow = 9, ncol = 4, scales = "free_y") +
geom_boxplot(width = 0.5, outlier.colour = NA) +
#geom_point(position = position_jitterdodge(dodge.width=0.5)
# , aes(colours = factor(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_text(size = 15)
, axis.title.y = element_text(size = 15)
, plot.title = element_text(size = 20, hjust = 0.5)
, strip.text.x = element_text(size = 15, colour = "black")
, legend.title = element_text(color = "black", size = 10)
, legend.text = element_text(size = 15)
, legend.direction = "vertical") +
labs(title = my_title1
, x = ""
, y = "Levels")+
stat_compare_means(comparisons = my_comparisons
, method = "wilcox.test"
, paired = F
, label = "p.format")
#p1
shift_legend2(p1)
dev.off()
######output
# Output plots as one pdf
cat("Output plots will be in:", output_boxplot)
pdf(output_boxplot, width = 20, height = 15)
my_title1 = "Boxplots: serum"
bxp <- ggboxplot(lf, x = "timepoint", y = "value",
color = "obesity", palette = c("#00BFC4", "#F8766D")) +
facet_wrap(~mediator, nrow = 7, ncol = 5, scales = "free_y", shrink = T)+
scale_y_log10()
bxp + 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_text(size = 15)
, axis.title.y = element_text(size = 15)
, plot.title = element_text(size = 20, hjust = 0.5)
, strip.text.x = element_text(size = 15, colour = "black")
, legend.title = element_text(color = "black", size = 20)
, legend.text = element_text(size = 15)
, legend.direction = "horizontal") +
labs(title = my_title1
, x = ""
, y = "Levels (Log10)")
#shift_legend2(bxp)
dev.off()