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added try catch for error handling

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This commit is contained in:
Tanushree Tunstall 2020-11-02 16:26:22 +00:00
parent 9c141326aa
commit 8033c1785f
3 changed files with 69 additions and 54 deletions
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73
boxplot_stat_function.R
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@ -5,27 +5,30 @@ getwd()
############################################################
# TASK: boxplots with stats
############################################################
is.error <- function(x) inherits(x, "try-error")
doMyPlotsStats <- function(df) {
mediators = levels(as.factor(df$mediator))
mediators = levels(as.factor(df$mediator))
plots <- list()
for (i in mediators) {
cat("Creating plot for:", i, "\n")
single=df[df$mediator==i,]
plots <- list()
max_y = max(single$value, na.rm = T)
#cat("Plotting:", i, "max_y:", max_y, "\n")
for (i in mediators) {
cat("Plotting:", i, "\n")
single=df[df$mediator==i,]
max_y = max(single$value, na.rm = T)
cat("Plotting:", i, "max_y:", max_y, "\n")
#----------
# boxplot
#----------
p = ggplot(single)+ geom_boxplot(aes(x = timepoint
, y = value
, color = obesity
#, palette = c("#00BFC4", "#F8766D")
))+
scale_colour_manual(values=c("#00BFC4", "#F8766D")) +
#----------
# boxplot
#----------
p = ggplot(single)+ 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
@ -36,11 +39,14 @@ doMyPlotsStats <- function(df) {
, legend.position = "none"
, plot.subtitle = element_text(size = 20, hjust = 0.5)
, plot.title = element_text(size = 20, hjust = 0.5)) +
labs(title = i)
labs(title = i)
#--------
# stats
#---------
stats_state <- try({
cat('Calculating stats for:', i, "\n")
#--------
# stats
#---------
stat_df <- single %>%
group_by(timepoint, mediator) %>%
wilcox_test(value ~ obesity, paired = F) %>%
@ -49,17 +55,24 @@ doMyPlotsStats <- function(df) {
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)))
plots[[i]] <- p2
}, silent=TRUE)
#print(stats_state)
if ( is.error(stats_state)) {cat("⚠️ Stats ERROR:", i, "\n")}
if ( ! is.error(stats_state)) {
cat('Adding stats to plot for:', i, "\n")
p = 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)))
}
return(plots)
plots[[i]] <- p
}
return(plots)
}
###############################################################