plotHeatmap {sights} | R Documentation

## Heat map

### Description

Plot heat map for each plate

### Usage

    plotHeatmap(plotMatrix, plateRows, plateCols, plotRows = NULL,
      plotCols = NULL, plotName = NULL, plotSep = TRUE, ...)

### Arguments

`plotMatrix` | Data frame or numeric matrix. Columns are plates, and rows are plate wells.
`plateRows, plateCols` | Number of rows/columns in plate.
`plotRows, plotCols` | Optional integer vector. Indicate which row/column numbers from the plotMatrix should be plotted. If NULL then all rows/columns from the plotMatrix are used.
`plotName` | Optional. Name of plotMatrix for plot title.
`plotSep` | Optional logical. Should plots be presented in separate windows? Default is TRUE.
`...` | Optional. Additional parameters passed to `geom_tile`.

### Details

Heat maps can be used to assess the existence of spatial bias on a plate by plate basis. Spatial bias can be visually subtle, however, and sometimes difficult to detect with heat maps. Auto-correlation plots (`plotAutoco`) can circumvent this problem.

### Value

Modifiable ggplot2 object or list of objects

### See Also

Other graphical devices: `plot3d`, `plotAutoco`, `plotBox`, `plotHist`, `plotIGFit`, `plotScatter`

### Examples

    ## load dataset
    data(ex_dataMatrix)

    ## plot raw data with graphs separated
    plotHeatmap(plotMatrix = ex_dataMatrix, plotCols = 5:10,
    plotName = 'Example', plateRows = 8, plateCols = 10)
    ## normalize data matrix using any method and store in new variable
    ex_normMatrix <- normZ(dataMatrix = ex_dataMatrix, dataCols = 5:10)
    ## plot normalized data with graphs together
    plotHeatmap(plotMatrix = ex_normMatrix, plotName = 'Example',
    plateRows = 8, plateCols = 10, plotSep = FALSE)

[Package sights version 1.8.1 Index]