buildXYData {Glimma} | R Documentation

## XY Data Object Builder

### Description

Common processing steps for both MA, XY and volcano plots. Expects a dataframe, `table`, which contains two columns labelled `xlab` and `ylab` as well as a unique identifier column labelled `gene`.

### Usage

    buildXYData(
      table,
      status,
      main,
      display.columns,
      anno,
      counts,
      xlab,
      ylab,
      status.cols,
      sample.cols,
      groups,
      transform.counts
    )

### Arguments

`table` | dataframe containing xlab and ylab columns for plotting.
`status` | vector of length `nrow(x)` indicating the status of each gene. By default genes in the summary plot are coloured based on its differential expression status using an adjusted p-value cutoff of 5% by calling the `limma::decideTests` function, where the value of -1 marks down-regulated genes, 0 marks genes with no expression difference, and 1 marks up-regulated genes.
`main` | character string for the main title of summary plot.
`display.columns` | character vector containing names of columns from `anno` from which to display in mouseover tooltips and table.
`anno` | dataframe with `nrow(x)` rows containing gene annotations.
`counts` | numeric matrix with `nrow(x)` rows containing gene expression values. This can be used to replace the gene counts from `dge$counts`, i.e. you may have log-rpkm values stored in a different object that you wish to use.
`xlab` | character string for the x-axis label of summary plot.
`ylab` | character string for the y-axis label of summary plot.
`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`.
`groups` | vector of length `ncol(dge)` representing categorisation of samples in expression plot.
`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".

### Value

object for XY plot internal use

[Package Glimma version 2.4.0 Index]