enrichplot源码阅读

YuLab-SMU/enrichplot/enrichplot/R/method-fortify.R

dotplot函数中使用as.data.frame(res <- as.data.frame(model))的泛型函数将enrichResult对象转换为data.frame对象，这其中就使用了enrichGO(pvalueCutoff = 0.01) 函数中pvalueCutoff参数设置的阈值对p.agjust进行筛选。res <- res[!is.na(res$Description), ]也是一个泛型函数，

点击查看S3对象的泛型和多态

fortify.internal

res <- as.data.frame(model)
res <- res[!is.na(res$Description), ]

res <- as.data.frame(model)

##' @method as.data.frame gseaResult
##' @export
as.data.frame.enrichResult <- function(x, ...) {
    x <- get_enriched(x)
    as.data.frame(x@result, ...)
}

res <- res[!is.na(res$Description), ]

##' @method [ enrichResult
##' @export
`[.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)
}

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)
}

可以看到pvalueCutoff <- object@pvalueCutoff这行代码是获取了enrichResult对象的pvalueCutoff这个属性。

Over <- Over[ Over$pvalue <= pvalueCutoff, ]
Over <- Over[ Over$p.adjust <= pvalueCutoff, ]

这里直接就使用了p.adjust < = pvalueCutoff的阈值进行过滤，并没有使用pvalue进行过滤的选项。

更改后的R包
BioinfoFungi/enrichplot2