101 lines
3.2 KiB
R
Executable file
101 lines
3.2 KiB
R
Executable file
#!/usr/bin/Rscript
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getwd()
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setwd("~/git/mosaic_2020/")
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getwd()
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############################################################
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# TASK: Boxplots with stats
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# for each mediator, at each timepoint by group
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# Handles some error: i.e will continue plotting even if there
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# is stats error. However, needs fixing see below point 1):
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# FIXME:
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# 1) For a given mediator, if there is error for ANY timepoint
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# stats will not be added for the entire plot!
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# 2) make the function more generic to take the following inputs
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# df, column, group
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# this way you can directly pass the log_calculated value column
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# To be handled in
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# next iteration!
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############################################################
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is.error <- function(x) inherits(x, "try-error")
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doMyPlotsStats <- function(df, custom_order=NULL) {
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if(!is.null(custom_order)){
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mediators = custom_order
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} else{
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mediators = levels(as.factor(df$mediator))
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}
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plots <- list()
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for (i in mediators) {
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cat("Creating plot for:", i, "\n")
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single=df[df$mediator==i,]
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max_y = max(single$value, na.rm = T)
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#cat("Plotting:", i, "max_y:", max_y, "\n")
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#----------
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# boxplot
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#----------
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p = ggplot(single)+ geom_boxplot(aes(x = timepoint
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, y = value
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, color = obesity
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#, palette = c("#00BFC4", "#F8766D")
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))+
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scale_colour_manual(values=c("#00BFC4", "#F8766D")) +
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theme(axis.text.x = element_text(size = 10)
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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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, legend.position = "none"
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, plot.subtitle = element_text(size = 14, hjust = 0.5)
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, plot.title = element_text(size = 14, hjust = 0.5)
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#, panel.grid.major = element_blank()
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, panel.grid.minor = element_blank()
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) +
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labs(title = i)
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#--------
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# stats
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#---------
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stats_state <- try({
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cat('Calculating stats for:', i, "\n")
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stat_df <- single %>%
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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_df$p_format = round(stat_df$p, digits = 2)
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stat_df <- stat_df %>%
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add_xy_position(x = "timepoint", dodge = 0.8)
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}, silent=TRUE)
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#print(stats_state)
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if ( is.error(stats_state)) {cat("⚠️ Stats ERROR:", i, "\n")}
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if ( ! is.error(stats_state)) {
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cat('Adding stats to plot for:', i, "\n")
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p = p + stat_pvalue_manual(stat_df
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#, y.position = max_y
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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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}
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plots[[i]] <- p
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}
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return(plots)
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}
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###############################################################
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