plotScatter: Scatter plot

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

Scatter plot

Description

Construct a scatter plot of all pairwise combinations of replicates

Usage

plotScatter(plotMatrix, repIndex, plotRows = NULL, plotCols = NULL,
  plotName = NULL, ...)

Arguments

plotMatrix	Data frame or numeric matrix. Columns are plates, and rows are plate wells.
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.
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.
...	Optional. Additional parameters passed to geom_point.

Details

Scatter plots with robust regression lines of replicate plates can reveal a kind of bias which acts independently of within-plate biases and which cannot be detected by heat maps (plotHeatmap) or auto-correlation plots (plotAutoco). A mixture of active and inactive features should produce a zero-correlation flat regression line within most of the range and a positively sloped line within the active range(s) at the extreme(s) of the distribution.

Value

List of modifiable ggplot2 objects

See Also

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

Examples

## load dataset
data(ex_dataMatrix)

## plot raw data
plotScatter(plotMatrix = ex_dataMatrix, repIndex = c(1,1,1), plotCols = 5:7,
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
plotScatter(plotMatrix = ex_normMatrix, repIndex = c(1,1,1), plotCols = 1:3,
plotName = 'Example')

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