Create volcano plot for Wilcoxon test result

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)
#> ℹ Running Wilcoxon rank-sum test
#> ✔ Running Wilcoxon rank-sum test ... done
#> 
plotVolcano(result, 1)
#> Warning: Removed 1 row containing missing values or values outside the scale range
#> (`geom_text_repel()`).