dotplot cannot use pvalue to filter

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Assessment

Difficulty
4/5
Estimated time
3-5 days
Newbie friendliness
35/100
Issue type
Feature
Clarity
Mostly clear
Activity status
Stale
Tech stack
r
Domain
data-visualization

Research direction

Start in R/method-fortify.R at fortify.internal and trace how dotplot obtains its data through as.data.frame.enrichResult and DOSE's get_enriched in enricher_internal.R. Compare the requested p-value filtering behavior with the existing pvalueCutoff and qvalueCutoff handling, then verify that the completed change lets dotplot apply the requested p-value filter.

Written by the indexing model from the issue text.

Description

Hi teacher:
I use dotplot to visualize enrichResult objects, but it cannot use pvalue to filter.

I found that in res <- as.data.frame(model) and res <- res[!is.na(res$Description), ] of the source code, It calls a generic function.

as.data.frame.enrichResult
[.enrichResult 

as.data.frame.enrichResult <- function(x, ...) {
    x <- get_enriched(x)
    as.data.frame(x@result, ...)
}
`[.enrichResult` <- function(x, i, j, asis = FALSE, ...) {
    x <- get_enriched(x)
    y <- x@result[i, j, ...]
    if (!asis)
        return(y)
    x@result <- y
    return(x)
}

Both of these two generic functions are called get_enriched.

x <- get_enriched(x)

get_enriched <- function(object) {
    Over <- object@result
    pvalueCutoff <- object@pvalueCutoff
    if (length(pvalueCutoff) != 0) {
        ## if groupGO result, numeric(0)
        Over <- Over[ Over$pvalue <= pvalueCutoff, ]
        Over <- Over[ Over$p.adjust <= pvalueCutoff, ]
    }
    qvalueCutoff <- object@qvalueCutoff
    if (length(qvalueCutoff) != 0) {
        if (! any(is.na(Over$qvalue))) {
            if (length(qvalueCutoff) > 0)
                Over <- Over[ Over$qvalue <= qvalueCutoff, ]
        }
    }
    object@result <- Over
    return(object)
}

However, there is no option to filter pvalue in function get_enriched. Can I add this filter parameter?

fortify.internal <- function(model, data, showCategory=5, by = "Count",
                             order=FALSE, drop=FALSE, split=NULL,colorBy="p.adjust", ...) {
    # res <- as.data.frame(model)
    res <- get_enriched(model,colorBy)
    # res <- res[!is.na(res$Description), ]
   ......
}
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R
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