fixed colours as well
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1ed09ac20b
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1 changed files with 92 additions and 9 deletions
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@ -9,7 +9,7 @@ getwd()
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#=============
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# Input
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#=============
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#source("boxplot_linear.R")
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source("boxplot_linear.R")
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#######################################################
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med_names = c("eotaxin3", "il12p70", "itac", "il13")
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lf_test = lf_fp_npa[lf_fp_npa$mediator%in%med_names,]
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@ -73,7 +73,8 @@ stat_npa3 <- lf_test %>%
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group_by(timepoint, mediator) %>%
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wilcox_test(value ~ obesity, paired = F) %>%
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add_significance("p")
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stat_npa3
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stat_npa3
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stat_npa3$p_format = round(stat_npa3$p, 3)
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stat_npa3 <- stat_npa3 %>%
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add_xy_position(x = "timepoint", dodge = 0.8)
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@ -108,6 +109,8 @@ head(stat_npa3_v2); head(stat_npa3)
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p3 = ggplot(lf_test)+ geom_boxplot(aes(x = timepoint
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, y = value
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, color = obesity))+
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scale_colour_manual(values=c("blue", "red")) +
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theme(axis.text.x = element_text(size = 15)
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, axis.text.y = element_text(size = 15
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, angle = 0
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@ -115,24 +118,25 @@ p3 = ggplot(lf_test)+ geom_boxplot(aes(x = timepoint
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, vjust = 0)
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, axis.title.x = element_blank()
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, axis.title.y = element_blank()
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, legend.position = "none"
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, strip.text.x = element_text(size = 20)
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, legend.position = "top"
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, legend.title = element_text(color = "black", size = 20)
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, legend.text = element_text(size = 15)
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, plot.subtitle = element_text(size = 20, hjust = 0.5)
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, plot.title = element_text(size = 20, hjust = 0.5)) +
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labs(title ="NPA")+
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#facet_wrap(~mediator, scales = "free")
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p3_build = ggbuild(p3)
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facet_wrap(~mediator, scales = "free", nrow = 2, ncol = 2)
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#p3
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p4 = p3 + stat_pvalue_manual(stat_npa3_v2
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, y.position = "my_y_pos"
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#, y.position = 50
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, label = "{p} {p.signif}"
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, label = "{p_format} {p.signif}"
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, hide.ns=T
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, tip.length = 0)+
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scale_y_continuous(expand = expansion(mult = c(0.05, 0.25)))
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p4
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#========================================
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#=======================================
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p3_build = ggplot_build(p3)
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p3_build$layout$panel_scales_y
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@ -150,3 +154,82 @@ get_facet_ymax <- function (x){
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}
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y_max_l = get_facet_ymax(p3_build); y_max_l
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#===============================================
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# facet wrap on actual data
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pdf("boxplot_stats.pdf", width = 20, height = 15)
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#=======
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# facet
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#=======
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#--------
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# wilcox stats
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#--------
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stat_npa3 <- lf_fp_npa %>%
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group_by(timepoint, mediator) %>%
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wilcox_test(value ~ obesity, paired = F) %>%
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add_significance("p")
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stat_npa3
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stat_npa3$p_format = round(stat_npa3$p, 3)
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stat_npa3 <- stat_npa3 %>%
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add_xy_position(x = "timepoint", dodge = 0.8)
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head(stat_npa3)
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#--------
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# summary stats
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#--------
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my_summary = lf_fp_npa %>%
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group_by(timepoint, mediator) %>%
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get_summary_stats(value)
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my_summary
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my_max_df = subset(my_summary
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, select = c("mediator", "timepoint"
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#, "obesity"
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, "max"))
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head(my_max_df); head(stat_npa3)
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#-----------------------------
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# merge my_max and stat_npa3
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#-----------------------------
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head(my_max_df)
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merging_cols = intersect(names(stat_npa3), names(my_max_df)); merging_cols
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stat_npa3_v2 = merge(stat_npa3, my_max_df, by = merging_cols, all.x = T)
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stat_npa3_v2$my_y_pos = (stat_npa3_v2$max)*1.2
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stat_npa3_v2$my_y_pos
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head(stat_npa3_v2); head(stat_npa3)
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p3 = ggplot(lf_fp_npa)+ geom_boxplot(aes(x = timepoint
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, y = value
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, color = obesity))+
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scale_colour_manual(values=c("blue", "red")) +
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scale_y_log10()+
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theme(axis.text.x = element_text(size = 15)
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, axis.text.y = element_text(size = 15
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, angle = 0
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, hjust = 1
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, vjust = 0)
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, axis.title.x = element_blank()
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, axis.title.y = element_blank()
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, strip.text.x = element_text(size = 20)
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, legend.position = "top"
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, legend.title = element_text(color = "black", size = 20)
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, legend.text = element_text(size = 15)
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, plot.subtitle = element_text(size = 20, hjust = 0.5)
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, plot.title = element_text(size = 20, hjust = 0.5)) +
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labs(title ="NPA")+
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facet_wrap(~mediator, scales = "free", nrow = 5, ncol = 7)
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#p3
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p4 = p3 + stat_pvalue_manual(stat_npa3_v2
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, y.position = "my_y_pos"
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#, y.position = 50
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, label = "{p_format} {p.signif}"
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, hide.ns=T
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, tip.length = 0) #+
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#scale_y_continuous(expand = expansion(mult = c(0.05, 0.25)))
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p4
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dev.off()
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