plotVolcano | R Documentation |
Volcano plot
plotVolcano(object, ...) ## S4 method for signature 'DESeqAnalysis' plotVolcano( object, i, alphaThreshold = NULL, baseMeanThreshold = NULL, lfcThreshold = NULL, genes = NULL, ntop = 0L, ... ) ## S4 method for signature 'DESeqResults' plotVolcano( object, direction = c("both", "up", "down"), alphaThreshold = NULL, baseMeanThreshold = NULL, lfcThreshold = NULL, genes = NULL, ntop = 0L, pointColor = c(downregulated = AcidPlots::lightPalette[["purple"]], upregulated = AcidPlots::lightPalette[["orange"]], nonsignificant = AcidPlots::lightPalette[["gray"]]), pointSize = 2L, pointAlpha = 0.8, limits = list(x = NULL, y = c(1e-10, 1L)), labels = list(title = TRUE, subtitle = NULL), histograms = FALSE )
object |
Object. |
i |
Indices specifying elements to extract or replace. Indices are For more information: help(topic = "Extract", package = "base") |
alphaThreshold |
|
baseMeanThreshold |
|
lfcThreshold |
|
genes |
|
ntop |
|
... |
Additional arguments. |
direction |
|
pointColor |
|
pointSize |
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pointAlpha |
|
limits |
|
labels |
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histograms |
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ggplot
.
plotVolcano,DESeqAnalysis-method
: Passes to DESeqResults
method, with gene2symbol
argument automatically defined.
Updated 2022-04-15.
Michael Steinbaugh, John Hutchinson, Lorena Pantano
CHBUtils::volcano_density_plot()
.
data(deseq) ## Get genes from DESeqDataSet. dds <- as.DESeqDataSet(deseq) genes <- head(rownames(dds)) print(genes) ## DESeqAnalysis ==== object <- deseq plotVolcano(object, i = 1L) ## Customize the colors. plotVolcano( object = object, i = 1L, pointColor = c( downregulated = "red", nonsignificant = "black", upregulated = "green" ) ) ## Directional support (up or down). plotVolcano( object = object, i = 1L, direction = "up", ntop = 5L ) plotVolcano( object = object, i = 1L, direction = "down", ntop = 5L ) ## Label genes manually. ## Note that either gene IDs or names (symbols) are supported. plotVolcano(object, i = 1L, genes = genes)
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