plotVolcano {rliger}

Create volcano plot for Wilcoxon test result

Description

plotVolcano is a simple implementation and shares most of arguments with other rliger plotting functions. plotEnhancedVolcano is a wrapper function of EnhancedVolcano::EnhancedVolcano(), which has provides substantial amount of arguments for graphical control. However, that requires the installation of package "EnhancedVolcano".

Usage

plotVolcano(
  result,
  group,
  logFCThresh = 1,
  padjThresh = 0.01,
  labelTopN = 20,
  dotSize = 2,
  dotAlpha = 0.8,
  legendPosition = "top",
  labelSize = 4,
  ...
)

plotEnhancedVolcano(result, group, ...)

Arguments

result

Data frame table returned by runWilcoxon

group

Selection of one group available from result$group

logFCThresh

Number for the threshold on the absolute value of the log2 fold change statistics. Default 1.

padjThresh

Number for the threshold on the adjusted p-value statistics. Default 0.01.

labelTopN

Number of top differential expressed features to be labeled on the top of the dots. Default 20.

dotSize, dotAlpha

Numbers for universal aesthetics control of dots. Default 2 and 0.8.

legendPosition

Text indicating where to place the legend. Choose from "top", "bottom", "left" or "right". Default "top".

labelSize

Size of labeled top features and line annotations. Default 4.

...

For plotVolcano, more theme setting arguments passed to .ggplotLigerTheme. For plotEnhancedVolcano, arguments passed to EnhancedVolcano::EnhancedVolcano().

Value

ggplot

Examples

result <- runMarkerDEG(pbmcPlot)
plotVolcano(result, 1)