volcano.ma.plot: Create MA and Volcano plots.
In rezakj/iCellR: Analyzing High-Throughput Single Cell Sequencing Data

volcano.ma.plot

R Documentation

Create MA and Volcano plots.

Description

This function takes the result of differential expression (DE) analysis and provides MA and volcano plots.

Usage

volcano.ma.plot(
  x = NULL,
  sig.value = "padj",
  sig.line = 0.1,
  plot.type = "volcano",
  x.limit = 2,
  y.limit = 2,
  limit.force = FALSE,
  scale.ax = TRUE,
  dot.size = 1.75,
  dot.transparency = 0.5,
  dot.col = c("#E64B35", "#3182bd", "#636363"),
  interactive = TRUE,
  out.name = "plot"
)

Arguments

`x`	A data frame containing differential expression (DE) analysis results.
`sig.value`	Choose from "pval" or "padj", default = "padj".
`sig.line`	A number to draw the line for the significant genes based on sig.value type, default = 0.1.
`plot.type`	Choose from "ma" or "volcano", default = "volcano".
`x.limit`	A number to set a limit for the x axis.
`y.limit`	A number to set a limit for the y axis.
`limit.force`	If set to TRUE the x.limit and y.limit will be forced, default = FALSE.
`scale.ax`	If set to TRUE the y axis will be scaled to include all the points, default = TRUE.
`dot.size`	A number for the size of the points in the plot, default = 1.75.
`dot.transparency`	Color transparency for points in "scatterplot" and "boxplot", default = 0.5.
`dot.col`	A set of three colors for the points in the volcano plot, default = c("#E64B35","#3182bd","#636363").
`interactive`	If set to TRUE an interactive HTML file will be created, default = TRUE.
`out.name`	If "interactive" is set to TRUE, the output name for HTML, default = "plot".