vsVolcano not displaying DESeq2 lfcShrink values?

[diegobah]

Can vsVolcano display shrunken lfc values from DESeq2?

Currently supplying such an object (e.g. dds <- DESeq(ddsCounts,betaPrior=TRUE)) to vsVolcano still produces output from lfcMLE of an unshrunk DESeq2 data object.

vsMAPlot displays shrunken LFC values correctly. Does vsVolcano generate a DESEq2 results object as part of its operation and if so how does it generate unshrunken lfc values?

[diegobah]

Looking into the code I noticed the LogFC value is generated rather than obtained from the DESeq object and thus the problem with representing pre-generated shrunken LFC values. The data aquisition for MAplot can be seen to pull the values directly.

getDeseqVolcano <- function(x, y, data, d.factor) {
if(missing(d.factor)) {
stop(
'This appears to be a DESeq object.
Please state d.factor variable.'
)
}
dat1 <- as.data.frame(colData(data))
dat2 <- fpm(data)
dat3 <- results(data, contrast = c(d.factor, y, x))
nam_x <- row.names(dat1[which(dat1[d.factor] == x),])
nam_y <- row.names(dat1[which(dat1[d.factor] == y),])
x <- rowMeans(dat2[, nam_x])
y <- rowMeans(dat2[, nam_y])
id <- row.names(data)
dat4 <- data.frame(id, x, y)
dat4$logFC <- log2(dat4$y / dat4$x)
dat4$pval <- dat3$pvalue
dat4$padj <- dat3$padj
dat4 <- dat4[complete.cases(dat4),]
return(dat4)
}

.getDeseqMA <- function(x, y, data, d.factor) {
if(missing(d.factor)) {
stop(
paste(
"This appears to be a DESeq object.",
"Please state "d.factor" variable."
)
)
}
dat1 <- as.data.frame(colData(data))
dat2 <- fpm(data)
dat3 <- results(data, contrast = c(d.factor, y, x))
nam_x <- row.names(dat1[which(dat1[d.factor] == x),])
nam_y <- row.names(dat1[which(dat1[d.factor] == y),])
x <- log10(rowMeans(dat2[, nam_x]) + 1)
y <- log10(rowMeans(dat2[, nam_y]) + 1)
id <- row.names(data)
dat4 <- data.frame(id, x, y)
dat4$A <- log10(dat3$baseMean)
#dat4$A <- 0.5 * log2(dat4$x * dat4$y)
dat4$M <- dat3$log2FoldChange
dat4$pval <- dat3$pvalue
dat4$padj <- dat3$padj
dat4 <- dat4[complete.cases(dat4), ]
return(dat4)
}