Plot Volcano

Plot Volcano

plotVolcano(object, ...)

# S4 method for DESeqResults
plotVolcano(object, alpha = NULL, ...)

# S4 method for data.frame
plotVolcano(object, alpha = 0.01, padj = TRUE,
  lfc = 1, genes = NULL, ntop = 0, direction = "both",
  shadeColor = "green", shadeAlpha = 0.25, pointColor = "gray",
  pointAlpha = 0.75, pointOutlineColor = "darkgray", histograms = TRUE)

Arguments

object	Object.
...	Additional arguments (for the S4 generic definition).
alpha	Alpha level cutoff used for coloring.
padj	Use P values adjusted for multiple comparisions.
lfc	Log fold change ratio (base 2) cutoff for coloring.
genes	Character vector of gene symbols to label.
ntop	Number of top genes to label.
direction	Plot up, down, or both (default) directions.
shadeColor	Shading color for bounding box.
shadeAlpha	Shading transparency alpha.
pointColor	Point color.
pointAlpha	Point transparency alpha.
pointOutlineColor	Point outline color.
histograms	Show LFC and P value histograms.

Value

Volcano plot arranged as grid (grid = TRUE), or show() individual ggplot (grid = FALSE).

See also

This function is an updated variant of CHBUtils::volcano_density_plot().

Other Differential Expression Plots: plotMA

Examples

# DESeqResults
plotVolcano(res, genes = "Sulf1")
#> Loading Ensembl annotations from AnnotationHub
#> 2017-10-27
#> EnsDB AH57770: Mus musculus Ensembl 90

# NOT RUN {
# data.frame
plotVolcano(as.data.frame(res))
# }