Override cldList stop if no statistical differences - r

Question

I'm trying to add cld to my data but the cldList stops working the moment it encounters statistical differences. My data has groups with both statistical differences and without, so I need a way to work around this issue. The cldList is part of the rcompanion package and is written as follow:
cldList = function(formula = NULL,
data = NULL,
comparison = NULL,
p.value = NULL,
threshold = 0.05,
print.comp = FALSE,
remove.space = TRUE,
remove.equal = TRUE,
remove.zero = TRUE,
swap.colon = TRUE,
swap.vs = FALSE,
...)
{
if(!is.null(formula)){
p.value = eval(parse(text=paste0("data","$",all.vars(formula[[2]])[1])))
comparison = eval(parse(text=paste0("data","$",all.vars(formula[[3]])[1])))
}
Comparison = (as.numeric(p.value) <= threshold)
if (sum(Comparison) == 0){stop("No significant differences.", call.=FALSE)} # THIS LINE HERE #
if(remove.space == TRUE) {comparison = gsub(" ", "", comparison)}
if(remove.equal == TRUE) {comparison = gsub("=", "", comparison)}
if(remove.zero == TRUE) {comparison = gsub("0", "", comparison)}
if(swap.colon == TRUE) {comparison = gsub(":", "-", comparison)}
if(swap.vs == TRUE) {comparison = gsub("vs", "-", comparison)}
names(Comparison) = comparison
if(print.comp == TRUE)
{Y = data.frame(Comparisons = names(Comparison),
p.value = p.value, Value=Comparison,
Threshold=threshold)
cat("\n", "\n")
print(Y)
cat("\n", "\n")}
MCL = multcompLetters(Comparison, ...)
Group = names(MCL$Letters)
Letter = as.character(MCL$Letters)
MonoLetter = as.character(MCL$monospacedLetters)
Z = data.frame(Group, Letter, MonoLetter)
return(Z)
}
Here's a portion of my data (output from another program):
dummy_df <-data.frame(target = c("A1","A1","A1","A1","A1","A1","A2","A2","A2","A2","A2","A2","A3","A3","A3","A3","A3","A3","A4","A4","A4","A4","A4","A4"),
comparison = c("a - b","a - c","a - d","b - c","b - d","c - d","a - b","a - c","a - d","b - c","b - d","c - d","e - c","e - d","e - f","c - d","c - f","d - f","e - c","e - d","e - f","c - d","c - f","d - f"),
significant = c("Yes","No","Yes","Yes","Yes","Yes","Yes","No","Yes","Yes","Yes","Yes","Yes","Yes","Yes","No","Yes","Yes","No","No","No","No","No","No"),
p.val = c( 0.04,0.06,0.04,0.04,0.04,0.04,0.04,0.06,0.04,0.04,0.04,0.04,0.04,0.04,0.04,0.06,0.04,0.04,0.06,0.06,0.06,0.06,0.06,0.06))
My code looks like this
i <- 1
targets <- data.frame(Genes = unique(dummy_df$target))
df <- data.frame()
df1 <- data.frame(Group = "No", Letter ="significant", MonoLetter = "differences")
while (i<=nrow(targets)) {
print(i)
df2 <-cldList(p.val~comparison, data = subset.data.frame(dummy_df, dummy_df$target==targets[i,]), threshold = 0.05)
print(df2)
df2$target <- targets[i,]
#print(df2)
df <- rbind(df, df2)
i <- i+1
}
I tried adding if (nrow(df2)==0) {df2 <- df1} after the cldList step to at least have the information about which targets aren't statistically difference, but without success.
Is there a workaround that makes the loop continue through all the targets? Ideally, the cldList output with the same letter for all Groups would be the goal.

Answer 1

I am the author of the cldList() function.
Unfortunately, the looping code you presented isn't working for me.
However, I can address the behavior of cldList() when there are no significant differences. The issue was that multcompLetters, which the function relies on, has different output when there are no significant differences.
EDIT: The function in the rcompanion package has been updated to return a data frame with the same letter for all groups when there are no significant differences. (rcompanion v. 2.4.13, CRAN.R-project.org/package=rcompanion
#### Examples
library(rcompanion)
Comparison = c("A-B", "A-C", "B-C")
Pvalue = c(0.04, 1, 1)
DataFrame = data.frame(Comparison, Pvalue)
cldList(Pvalue ~ Comparison, data=DataFrame)
### Group Letter MonoLetter
### 1 A a a
### 2 B b b
### 3 C ab ab
Comparison2 = c("A-B", "A-C", "B-C")
Pvalue2 = c(1, 1, 1)
DataFrame2 = data.frame(Comparison2, Pvalue2)
cldList(Pvalue2 ~ Comparison2, data=DataFrame2)
### Group Letter MonoLetter
### 1 A a a
### 2 B a a
### 3 C a a