plotAutoco {sights} | R Documentation

## Auto-correlation

### Description

Plot auto-correlation for each plate

### Usage

    plotAutoco(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_path`.

### Details

Auto-correlation plots can be used to identify spatial bias. Non-zero auto-correlations indicate within-plate bias, namely that proximal wells within-plates are correlated and that the measured intensity of a feature depends partially on its well location in the plate. Cyclical patterns of auto-correlation, in particular indicate within-plate spatial bias. Normalization methods that produce auto-correlations close to zero indicate the removal of spatial bias.

### Value

Modifiable ggplot2 object or list of objects

### See Also

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

### Examples

    ## load dataset
    data(ex_dataMatrix)

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

[Package sights version 1.8.1 Index]