degPlot {DEGreport} | R Documentation

## Plot top genes allowing more variables to color and shape points

### Description

Plot top genes allowing more variables to color and shape points

### Usage

    degPlot(
      dds,
      xs,
      res = NULL,
      n = 9,
      genes = NULL,
      group = NULL,
      batch = NULL,
      metadata = NULL,
      ann = c("geneID", "symbol"),
      slot = 1L,
      log2 = TRUE,
      xsLab = xs,
      ysLab = "abundance",
      color = "black",
      groupLab = group,
      batchLab = batch,
      sizePoint = 1
    )

### Arguments

`dds` | DESeq2::DESeqDataSet object or SummarizedExperiment or Matrix or data.frame. In case of a DESeqDataSet object, always the normalized expression will be used from `counts(dds, normalized = TRUE)`.
`xs` | Character, colname in colData that will be used as X-axes.
`res` | DESeq2::DESeqResults object.
`n` | Integer number of genes to plot from the `res` object. It will take the top N using padj values to order the table.
`genes` | Character of gene names matching rownames of count data.
`group` | Character, colname in colData to color points and add different lines for each level.
`batch` | Character, colname in colData to shape points, normally used by batch effect visualization.
`metadata` | Metadata in case dds is a matrix.
`ann` | Columns in rowData (if available) used to print gene names. First element in the vector is the column name in rowData that matches the row.names of the `dds` or `count` object. Second element in the vector is the column name in rowData that it will be used as the title for each gene or feature figure.
`slot` | Name of the slot to use to get count data.
`log2` | Whether to apply or not log2 transformation.
`xsLab` | Character, alternative label for x-axis (default: same as xs)
`ysLab` | Character, alternative label for y-axis..
`color` | Color to use to plot groups. It can be one color, or a palette compatible with `ggplot2::scale_color_brewer()`.
`groupLab` | Character, alternative label for group (default: same as group).
`batchLab` | Character, alternative label for batch (default: same as batch).
`sizePoint` | Integer, indicates the size of the plotted points (default 1).

### Value

ggplot showing the expresison of the genes

### Examples

    data(humanGender)
    library(DESeq2)
    idx <- c(1:10, 75:85)
    dse <- DESeqDataSetFromMatrix(assays(humanGender)[[1]][1:1000, idx],
      colData(humanGender)[idx,], design=~group)
    dse <- DESeq(dse)
    degPlot(dse, genes = rownames(dse)[1:10], xs = "group")
    degPlot(dse, genes = rownames(dse)[1:10], xs = "group", color = "orange")
    degPlot(dse, genes = rownames(dse)[1:10], xs = "group", group = "group",
            color = "Accent")

[Package DEGreport version 1.30.3 Index]