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added boxplot_stat_log.R to generate graphs with log data and stats

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Tanushree Tunstall 2020-11-02 14:28:52 +00:00
parent 550e8b2c50
commit b8ff7995ac
6 changed files with 249 additions and 10 deletions
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89
boxplot_stat_function_test.R
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@ -22,8 +22,16 @@ pdf(output_boxplot_stats, width=22, height=16)
#med_names = c("eotaxin3", "il12p70", "itac", "il13")
#lf_test = lf_fp_npa[lf_fp_npa$mediator%in%med_names,]
#baz=cowplot::plot_grid(plotlist=foo, align = 'hv', ncol=2, nrow=2)
foo_annot = annotate_figure(foo
baz=cowplot::plot_grid(plotlist=foo, align = 'hv', ncol=2, nrow=2)
baz
sam_plot = ggpubr::ggarrange(plotlist = foo
, align = "hv"
, ncol = 7
, nrow = 5
, common.legend = T)
sam_plot
foo_annot = annotate_figure(sam_plot
, top = text_grob(my_sample_name
, color = "blue"
, face = "bold"
@ -41,3 +49,80 @@ foo_annot = annotate_figure(foo
foo_annot
dev.off()
##################################################################
# ind components of function
my_sample_name = "SAM"
to_remove = c("ifna2a"
, "il29")
lf_fp_sam2 = lf_fp_sam[!lf_fp_sam$mediator%in%to_remove,]
lf_fp_sam3 = lf_fp_sam[lf_fp_sam$mediator%in%to_remove,]
df_test = lf_fp_sam3
df_test = lf_fp_sam2
table(df_test$mediator)
p = ggplot(df_test)+ geom_boxplot(aes(x = timepoint
, y = value
, color = obesity
#, palette = c("#00BFC4", "#F8766D")
))+
scale_colour_manual(values=c("#00BFC4", "#F8766D")) +
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 = "TEST")
p
#--------
# stats
#---------
to_remove = c("ifna2a"
, "il29")
lf_fp_sam3 = lf_fp_sam[lf_fp_sam$mediator%in%to_remove,]
lf_fp_sam4 = lf_fp_sam3[lf_fp_sam3$timepoint == "t3",]
table(lf_fp_sam4$timepoint)
wilcox_test(value~obesity, data = lf_fp_sam4)
table(lf_fp_sam3$mediator, lf_fp_sam3$timepoint)
time = c("t3")
lf_fp_sam3 = lf_fp_sam3[!lf_fp_sam3$timepoint%in%time,]
table(lf_fp_sam3$mediator, lf_fp_sam3$timepoint)
med = c("il29")
time2 = c("t2")
lf_fp_sam3 = lf_fp_sam3[!lf_fp_sam3$mediator%in%med && lf_fp_sam3$timepoint%in%time2,]
table(lf_fp_sam3$mediator, lf_fp_sam3$timepoint)
df_test = lf_fp_sam3
table(df_test$mediator)
stat_df <- df_test %>%
group_by(timepoint, mediator) %>%
wilcox_test(value ~ obesity, paired = F) %>%
add_significance("p")
stat_df$p_format = round(stat_df$p, digits = 3)
stat_df <- stat_df %>%
add_xy_position(x = "timepoint", dodge = 0.8)
p2 = p + stat_pvalue_manual(stat_df
#, y.position = max_y
, label = "{p_format} {p.signif}"
, hide.ns = T
, tip.length = 0)+
scale_y_continuous(expand = expansion(mult = c(0.05, 0.25)))
p2