plotBox: Boxplot
In sights: Statistics and dIagnostic Graphs for HTS

Description Usage Arguments Details Value See Also Examples

Construct an ordered boxplot for each plate

1 2	plotBox(plotMatrix, plotRows = NULL, plotCols = NULL, plotName = NULL, repIndex = NULL, plotSep = TRUE, ...)

`plotMatrix`	Data frame or numeric matrix. Columns are plates, and rows are plate wells.
`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.
`repIndex`	Optional. Vector of labels indicating replicate group. Each index in the vector matches the corresponding column of plotMatrix. If NULL then all plates are plotted together without grouping.
`plotSep`	Optional logical. Should plots of different replicate groups be presented in separate windows? Default is TRUE. Does not apply if repIndex is NULL.
`...`	Optional. Additional parameters passed to `geom_boxplot`.

Box plots can be used to identify scaling shifts among replicates and view the general distribution of data among all plates.

Modifiable ggplot2 object or list of objects

Other graphical devices: plot3d, plotAutoco, plotHeatmap, plotHist, plotIGFit, plotScatter

## load dataset
data(ex_dataMatrix)

## plot raw data
plotBox(plotMatrix = ex_dataMatrix, repIndex = c(1,1,1,2,2,2), 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
plotBox(plotMatrix = ex_normMatrix, repIndex = c(1,1,1,2,2,2), plotName = 'Example')