plotPeak2GeneHeatmap | R Documentation |
This function plots side by side heatmaps of linked ATAC and Gene regions from addPeak2GeneLinks
.
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")
)
ArchRProj |
An |
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 |
palGroup |
A color palette describing the colors in |
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. |
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