plotPeak2GeneHeatmap: Plot Peak2Gene Heatmap from an ArchRProject
In haibol2016/ArchR_debug: Analyzing single-cell regulatory chromatin in R.

plotPeak2GeneHeatmap

R Documentation

Plot Peak2Gene Heatmap from an ArchRProject

Description

This function plots side by side heatmaps of linked ATAC and Gene regions from addPeak2GeneLinks.

Usage

plotPeak2GeneHeatmap(
  ArchRProj = NULL,
  corCutOff = 0.45,
  FDRCutOff = 1e-04,
  varCutOffATAC = 0.25,
  varCutOffRNA = 0.25,
  k = 25,
  nPlot = 25000,
  limitsATAC = c(-2, 2),
  limitsRNA = c(-2, 2),
  groupBy = "Clusters",
  palGroup = NULL,
  palATAC = paletteContinuous("solarExtra"),
  palRNA = paletteContinuous("blueYellow"),
  verbose = TRUE,
  returnMatrices = FALSE,
  seed = 1,
  logFile = createLogFile("plotPeak2GeneHeatmap")
)

Arguments

`ArchRProj`	An `ArchRProject` object.
`corCutOff`	A numeric describing the minimum numeric peak-to-gene correlation to return.
`FDRCutOff`	A numeric describing the maximum numeric peak-to-gene false discovery rate to return.
`varCutOffATAC`	A numeric describing the minimum variance quantile of the ATAC peak accessibility when selecting links.
`varCutOffRNA`	A numeric describing the minimum variance quantile of the RNA gene expression when selecting links.
`k`	An integer describing the number of k-means clusters to group peak-to-gene links prior to plotting heatmaps.
`nPlot`	An integer describing the maximum number of peak-to-gene links to plot in heatmap.
`limitsATAC`	An integer describing the maximum number of peak-to-gene links to plot in heatmap.
`limitsRNA`	An integer describing the maximum number of peak-to-gene links to plot in heatmap.
`groupBy`	The name of the column in `cellColData` to use for labeling KNN groupings. The maximum group appeared in the KNN groupings is used.
`palGroup`	A color palette describing the colors in `groupBy`. For example, if groupBy = "Clusters" try paletteDiscrete(ArchRProj$Clusters) for a color palette.
`palATAC`	A color palette describing the colors to be used for the ATAC heatmap. For example, paletteContinuous("solarExtra").
`palRNA`	A color palette describing the colors to be used for the RNA heatmap. For example, paletteContinuous("blueYellow").
`verbose`	A boolean value that determines whether standard output should be printed.
`returnMatrices`	A boolean value that determines whether the matrices should be returned with kmeans id versus plotting.
`seed`	A number to be used as the seed for random number generation. It is recommended to keep track of the seed used so that you can reproduce results downstream.
`logFile`	The path to a file to be used for logging ArchR output.