plotAutoco: Auto-correlation

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

Auto-correlation

Description

Plot auto-correlation for each plate

Usage

plotAutoco(plotMatrix, plateRows, plateCols, plotRows = NULL,
  plotCols = NULL, plotName = NULL, plotSep = TRUE, ...)

Arguments

plotMatrix	Data frame or numeric matrix. Columns are plates, and rows are plate wells.
plateRows, plateCols	Number of rows/columns in plate.
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.
...	Optional. Additional parameters passed to geom_path.

Details

Auto-correlation plots can be used to identify spatial bias. Non-zero auto-correlations indicate within-plate bias, namely that proximal wells within-plates are correlated and that the measured intensity of a feature depends partially on its well location in the plate. Cyclical patterns of auto-correlation, in particular indicate within-plate spatial bias. Normalization methods that produce auto-correlations close to zero indicate the removal of spatial bias.

Value

Modifiable ggplot2 object or list of objects

See Also

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

Examples

## load dataset
data(ex_dataMatrix)

## plot raw data
plotAutoco(plotMatrix = ex_dataMatrix, plateRows = 8, plateCols = 10,
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
plotAutoco(plotMatrix = ex_normMatrix, plotName = 'Example',
plateRows = 8, plateCols = 10, plotSep = FALSE)

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