plotBox: Boxplot

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

Boxplot

Description

Construct an ordered boxplot for each plate

Usage

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

Arguments

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.

Details

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

Value

Modifiable ggplot2 object or list of objects

See Also

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

Examples

## 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')

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