plotSights {sights} | R Documentation

## Graphical devices

### Description

Apply any of the available SIGHTS graphical devices

### Usage

    plotSights(plotMethod, plotMatrix, plateRows, plateCols, repIndex = NULL,
      plotRows = NULL, plotCols = NULL, plotName = NULL, plotSep = TRUE,
      plotAll = FALSE, colNames = NULL, ...)

### Arguments

`plotMethod` | Plotting method name from SIGHTS ('3d', 'Autoco', 'Box', 'Heatmap', 'Hist', 'IGFit', or 'Scatter').
`plotMatrix` | Data frame or numeric matrix. Columns are plates, and rows are plate wells. For plotMethod 'Hist', this is a p-value matrix with each column a single sample.
`plateRows, plateCols` | Number of rows/columns in plate. Applies to plotMethods '3d', 'Autoco' and 'Heatmap'.
`repIndex` | Vector of labels indicating replicate group. Each index in the vector matches the corresponding column of plotMatrix. Applies to plotMethods 'Box', 'Scatter' and 'IGFit'.
`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. Applies to plotMethods 'Autoco', 'Box', 'Hist' and 'Heatmap'. For 'Box', each replicate group is presented in a separate window and it only applies if repIndex is not NULL.
`plotAll` | Optional logical. Should all p-values be plotted together? Default is FALSE. Applies to plotMethod 'Hist'.
`colNames` | Optional. Names of plotCols for plot title. Applies to plotMethod 'Hist'.
`...` | Optional. Additional parameters passed to `ggplot` functions.

### Details

One of the following SIGHTS graphical devices may be chosen: `plot3d`, `plotAutoco`, `plotBox`, `plotHeatmap`, `plotHist`, `plotIGFit`, or `plotScatter`. See their individual help pages for more details.

### Value

List of lattice objects for 'plot3d'. Modifiable ggplot2 object or list of objects for all others.

### References

Murie et al. (2015). Improving detection of rare biological events in high-throughput screens. Journal of Biomolecular Screening, 20(2), 230-241.

### See Also

Other SIGHTS functions: `normSights`, `statSights`

### Examples

    ## load dataset
    data(ex_dataMatrix)

    ## normalize data matrix using any method and store in new variable
    ex_normMatrix <- normSights(normMethod = 'RobZ', dataMatrix = ex_dataMatrix,
    dataCols = 5:10, wellCorrection = TRUE)
    ## choose a graphical device and provide relevant information
    plotSights(plotMethod = 'Autoco', plotMatrix = ex_normMatrix,
    plotName = 'Example', plateRows = 8, plateCols = 10)

[Package sights version 1.6.0 Index]