plotHeatmap: Heat map

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

Heat map

Description

Plot heat map for each plate

Usage

plotHeatmap(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_tile.

Details

Heat maps can be used to assess the existence of spatial bias on a plate by plate basis. Spatial bias can be visually subtle, however, and sometimes difficult to detect with heat maps. Auto-correlation plots (plotAutoco) can circumvent this problem.

Value

Modifiable ggplot2 object or list of objects

See Also

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

Examples

## load dataset
data(ex_dataMatrix)

## plot raw data with graphs separated
plotHeatmap(plotMatrix = ex_dataMatrix, plotCols = 5:10,
plotName = 'Example', plateRows = 8, plateCols = 10)
## normalize data matrix using any method and store in new variable
ex_normMatrix <- normZ(dataMatrix = ex_dataMatrix, dataCols = 5:10)
## plot normalized data with graphs together
plotHeatmap(plotMatrix = ex_normMatrix, plotName = 'Example',
plateRows = 8, plateCols = 10, plotSep = FALSE)

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