plotSights: Graphical devices

In eg-r/sights: Statistics and dIagnostic Graphs for HTS

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)

eg-r/sights documentation built on Jan. 28, 2023, 12:17 a.m.