plotSights: Graphical devices
In sights: Statistics and dIagnostic Graphs for HTS

Description Usage Arguments Details Value References See Also Examples

Apply any of the available SIGHTS graphical devices

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

`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.

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.

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

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

Other SIGHTS functions: normSights, statSights

## 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)