plotEISA {eisaR} | R Documentation

## Visualize the results from an exon-intron split analysis.

### Description

`plotEISA` takes the return value from `runEISA` and generates a scatterplot of intronic versus exonic changes.

### Usage

    plotEISA(
      x,
      contrast = c("ExIn", "none"),
      minLfc = NULL,
      maxFDR = 0.05,
      genecolors = c("#E41A1C", "#497AB3", "#222222"),
      ...
    )

### Arguments

`x` | `list` with EISA results, typically the return value from `runEISA`
`contrast` | one of `"ExIn"` or `"none"`. If `"ExIn"` (the default), genes that significantly differ between exonic and intronic changes are highlighted. `"none"` turns off gene highlighting.
`minLfc` | `NULL` or `numeric(1)` with the minimal absolute log2 fold change to color a gene. If `NULL` (the default), no fold changes are not used to select genes for highlighting.
`maxFDR` | `numeric(1)` with maximal false discovery rate for gene highlighting.
`genecolors` | Vector of length three specifying the colors to use for genes that are significantly up, down or unchanged.
`...` | further arguments past to `plot()`. Parameters that will be set automatically unless given in the arguments are: pch : plot symbol (default: `"."`) cex : plot symbol expansion factor (default: `2`) col : plot symbol color (default: according to `contrast` and `genecolors`) xlab/ylab : axis labels

### Value

`NULL` (invisibly)

### Author(s)

Michael Stadler

### Examples

      # see the help for runEISA() for a full example

[Package eisaR version 0.99.11 Index]