glimmaVolcano.DESeqDataSet {Glimma} | R Documentation

## Glimma Volcano Plot

### Description

Draws a two-panel interactive volcano plot from an DESeqDataSet object. This is a special case of the `glimmaXY` plot.

### Usage

    ## S3 method for class 'DESeqDataSet'
    glimmaVolcano(
      x,
      counts = DESeq2::counts(x),
      groups = extractGroups(colData(x)),
      status = NULL,
      anno = NULL,
      display.columns = NULL,
      status.cols = c("#1052bd", "silver", "#cc212f"),
      sample.cols = NULL,
      transform.counts = c("logcpm", "cpm", "rpkm", "none"),
      main = "Volcano Plot",
      xlab = "logFC",
      ylab = "negLog10PValue",
      html = NULL,
      width = 920,
      height = 920,
      ...
    )

### Arguments

`x` | DESeqDataSet object from which summary statistics are extracted from to create summary (left) plot.
`counts` | numeric matrix with nrow(x) rows containing gene expression values.
`groups` | vector/factor representing the experimental group for each sample; see `extractGroups` for default value.
`status` | vector of length nrow(x) indicating the status of each gene.
`anno` | dataframe with `nrow(x)` rows containing gene annotations.
`display.columns` | character vector containing names of columns from `anno` from which to display in mouseover tooltips and table.
`status.cols` | vector of length 3 containing valid CSS strings for colours associated with `status` in the order of -1, 0 and 1.
`sample.cols` | character vector of length `ncol(counts)` containing valid CSS strings for colours associated with each sample to be displayed on the expression plot. If left unspecified, samples will be coloured according to `groups`.
`transform.counts` | the type of transformation used on the counts - "logcpm" for using `edgeR::cpm(counts, log=TRUE)`; "cpm" for `edgeR::cpm(counts)`; "rpkm" for `edgeR::rpkm(counts)`; "logrpkm" for `edgeR::rpkm(counts, log=TRUE)`; and "none" for no transformation). Defaults to "logcpm".
`main` | character string for the main title of summary plot.
`xlab` | character string for the x-axis label of summary plot.
`ylab` | character string for the y-axis label of summary plot.
`html` | character string for naming HTML file for exportation of widget. The extension should be included in the file name e.g. "file.html".
`width` | numeric value indicating width of widget in pixels.
`height` | numeric value indicating width of height in pixels.
`...` | additional unused arguments.

### Details

The summary plot on the left represents gene-wise log-fold-change (logFC) on the x-axis versus `-log10(pvalue)`. The expression plot on the right displays sample expression values for a single gene. Interactions with the htmlwidget include clicking on genes (points) in the summary plot to bring up associated sample expression values in the expression plot, as well as the summary statistics in the table below. Alternatively, users can interact with the table by clicking on genes (rows) to highlight genes in the summary plot, as well as bring up associated sample expression values in the expression plot. Briefly, other interactive features include a search box for the table, buttons to save plots and data (summary statistics and expression values), additional pop-up information when hovering on points in plots, and rescaling of the y-axis in the expression plot.

### Value

htmlwidget object or `NULL` if `html` argument is specified.

### Author(s)

Hasaru Kariyawasam, Shian Su and Oliver Voogd

### See Also

`glimmaVolcano`, `glimmaVolcano.MArrayLM`, `glimmaVolcano.DGEExact`, `glimmaVolcano.DGELRT`

### Examples

    dge <- readRDS(
      system.file("RNAseq123/dge.rds", package = "Glimma"))

    dds <- DESeq2::DESeqDataSetFromMatrix(
      countData = dge$counts,
      colData = dge$samples,
      rowData = dge$genes,
      design = ~group
    )

    dds <- DESeq2::DESeq(dds, quiet=TRUE)
    glimmaVolcano(dds)

[Package Glimma version 2.4.0 Index]