plotTrajectoryHeatmap | R Documentation |
This function will plot a heatmap of the results from getTrajectory
plotTrajectoryHeatmap(
seTrajectory = NULL,
varCutOff = 0.9,
maxFeatures = 25000,
scaleRows = TRUE,
limits = c(-1.5, 1.5),
grepExclude = NULL,
pal = NULL,
labelMarkers = NULL,
labelTop = 50,
labelRows = FALSE,
rowOrder = NULL,
useSeqnames = NULL,
returnMatrix = FALSE,
force = FALSE,
logFile = createLogFile("plotTrajectoryHeatmap")
)
seTrajectory |
A |
varCutOff |
The "Variance Quantile Cutoff" to be used for identifying the top variable features across the given trajectory. Only features with a variance above the provided quantile will be retained. |
maxFeatures |
The maximum number of features, ordered by variance, to consider from |
scaleRows |
A boolean value that indicates whether row-wise z-scores should be computed on the matrix provided by |
limits |
A numeric vector of two numbers that represent the lower and upper limits of the heatmap color scheme. |
grepExclude |
A character vector or string that indicates the |
pal |
A custom continuous palette (see |
labelMarkers |
A character vector listing the |
labelTop |
A number indicating how many of the top N features, based on variance, in |
labelRows |
A boolean value that indicates whether all rows should be labeled on the side of the heatmap. |
rowOrder |
If wanting to set the order of rows to be plotted, the indices (integer or character correpsonding to rownmaes) can be provided here. |
useSeqnames |
A character vector that indicates which |
returnMatrix |
A boolean value that indicates whether the final heatmap matrix should be returned in lieu of plotting the actual heatmap. |
force |
If useSeqnames is longer than 1 if matrixClass is "Sparse.Assays.Matrix" to continue. This is not recommended because these matrices can be in different units. |
logFile |
The path to a file to be used for logging ArchR output. |
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