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making it work with function and ggarrange to combine plots

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This commit is contained in:
Tanushree Tunstall 2020-10-31 20:43:07 +00:00
parent 6575fc7aba
commit dd54f10ad8
1 changed files with 42 additions and 30 deletions
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68
boxplot_stat_function.R
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@ -5,14 +5,14 @@ getwd()
############################################################ ############################################################
# TASK: boxplots with stats # TASK: boxplots with stats
############################################################ ############################################################
doMyPlots <- function(x, title = "TEST") { doMyPlots <- function(df) {
mediators = levels(as.factor(x$mediator)) mediators = levels(as.factor(df$mediator))
plots <- list() plots <- list()
for (i in mediators) { for (i in mediators) {
cat("Plotting:", i, "\n") cat("Plotting:", i, "\n")
single=x[x$mediator==i,] single=df[df$mediator==i,]
max_y = max(single$value, na.rm = T) max_y = max(single$value, na.rm = T)
cat("Plotting:", i, "max_y:", max_y, "\n") cat("Plotting:", i, "max_y:", max_y, "\n")
@ -20,13 +20,12 @@ doMyPlots <- function(x, title = "TEST") {
#---------- #----------
# boxplot # boxplot
#---------- #----------
p2 = ggboxplot(single p = ggplot(single)+ geom_boxplot(aes(x = timepoint
, x = "timepoint" , y = value
, y = "value" , color = obesity
, color = "obesity" #, palette = c("#00BFC4", "#F8766D")
#, palette = c("blue", "red") ))+
, 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
@ -38,31 +37,29 @@ doMyPlots <- function(x, title = "TEST") {
, 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 = i) labs(title = i)
#-------- #--------
# stats # stats
#--------- #---------
stat_npa2 <- single %>% stat_df <- single %>%
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_npa2 stat_df
stat_npa2 <- stat_npa2 %>% stat_df <- stat_df %>%
add_xy_position(x = "timepoint", dodge = 0.8) add_xy_position(x = "timepoint", dodge = 0.8)
cat("printing p")
p2 = p2 + stat_pvalue_manual(stat_npa2 p2 = p + stat_pvalue_manual(stat_df
#, y.position = max_y #, y.position = max_y
, label = "{p} {p.signif}" , label = "{p} {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)))
scale_x_discrete()
plots[[i]] <- p2 plots[[i]] <- p2
} }
return(plots) return(plots)
} }
############################################################### ###############################################################
@ -75,7 +72,7 @@ source("boxplot_linear.R")
#============= #=============
outfile_bp = paste0("boxplots_TEST", ".pdf") outfile_bp = paste0("boxplots_TEST", ".pdf")
output_boxplot_stats = paste0(outdir_plots, outfile_bp); output_boxplot_stats output_boxplot_stats = paste0(outdir_plots, outfile_bp); output_boxplot_stats
pdf(output_boxplot_stats, width=22, height=16) #pdf(output_boxplot_stats, width=22, height=16)
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,]
@ -83,8 +80,8 @@ lf_test = lf_fp_npa[lf_fp_npa$mediator%in%med_names,]
foo=doMyPlots(lf_test) foo=doMyPlots(lf_test)
#baz=cowplot::plot_grid(plotlist=foo, align = 'hv', ncol=2, nrow=2) #baz=cowplot::plot_grid(plotlist=foo, align = 'hv', ncol=2, nrow=2)
baz baz
dev.off() #dev.off()
##################################################################
#========================= #=========================
# entire sample_type data # entire sample_type data
#========================= #=========================
@ -93,9 +90,24 @@ outfile_bp = paste0("boxplots_stats_", my_sample_type, ".pdf")
output_boxplot_stats = paste0(outdir_plots, outfile_bp); output_boxplot_stats output_boxplot_stats = paste0(outdir_plots, outfile_bp); output_boxplot_stats
pdf(output_boxplot_stats, width=22, height=16) pdf(output_boxplot_stats, width=22, height=16)
bar=doMyPlots(lf_fp_npa) #===========================
#bang=cowplot::plot_grid(plotlist=bar, align = 'hv', ncol=7, nrow=5) # combine: ggpubr::ggarrange
#bang #===========================
plots_npa = doMyPlots(lf_fp_npa)
npa_plot = ggpubr::ggarrange(plotlist = plots_npa
, align = "hv"
, ncol = 7
, nrow = 5
, common.legend = T)
#npa_plot
npa_plot_annot = annotate_figure(npa_plot
, top = text_grob(my_sample_type, color = "purple", face = "bold", size = 14)
, bottom = text_grob("Mosaic data\nFlu positive adults (n=133)"
, color = "blue"
, hjust = 1, x = 0.98, face = "italic", size = 10)
, left = text_grob("Levels (pg/ml)", color = "black", rot = 90, size = 18)
#, right = "I'm done, thanks :-)!",
#, fig.lab = "Figure 1", fig.lab.face = "bold"
)
npa_plot_annot
dev.off() dev.off()