stains


  This is a data set describing the display parameters used to plot
  cytoband data.


datasets

The ChromHeatMap package can be used to plot genome-wide data (e.g. expression, CGH, SNP) along each strand of a given chromosome as a heat map. The generated heat map can be used to interactively identify probes and genes of interest.

Tim F Rayner

ChromHeatMap

Heat map plotting by genome coordinate

stains function

A data frame with one row per cytoband type, and the following columns:
  <ul>
<li>typeThe cytoband type. This must correspond to the "stain"
      column in the cytoband data frame (see the <code>cytobands</code> documentation). </li>
<li>bandcolThe shade of gray used to colour the cytobands. A
      number between 0 (black) and 1 (white). Passed as the "col"
      argument to <code>rect</code>. </li>
<li>textcolThe shade of gray used for the cytoband text labels. A
      number between 0 (black) and 1 (white). Passed as the "col"
      argument to <code>text</code>. </li>
<li>banddensThe shading density to use for the band
    colour. Passed as the "density" argument to <code>rect</code>. </li>
<li>bandbordThe shade of gray used for the plotted cytoband
      borders. A number between 0 (black) and 1 (white). Passed as the
      "border" argument to <code>rect</code>.
  </li>
</ul> 

Format

Developed based on the design of the idiogram Bioconductor package

stains: Cytoband display information

Description

Usage

Arguments

Format

Source