Plot a Heatmap of Features across a Trajectory — plotTrajectoryHeatmap • ArchR

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")
)

Arguments

seTrajectory: A SummarizedExperiment object that results from calling getTrajectory().
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 useMatrix when generating a trajectory. This prevents smoothing a large number number of features which can be very time consuming.
scaleRows: A boolean value that indicates whether row-wise z-scores should be computed on the matrix provided by seTrajectory.
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 rownames or a specific pattern that identifies rownames from seTrajectory to be excluded from the heatmap.
pal: A custom continuous palette (see paletteContinuous()) used to override the default continuous palette for the heatmap.
labelMarkers: A character vector listing the rownames of seTrajectory that should be labeled on the side of the heatmap.
labelTop: A number indicating how many of the top N features, based on variance, in seTrajectory should be labeled on the side of the heatmap.
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 seqnames should be plotted in the heatmap. Features from seqnames that are not listed will be ignored. In the context of a Sparse.Assays.Matrix, such as a matrix containing chromVAR deviations, the seqnames do not correspond to chromosomes, rather they correspond to the sub-portions of the matrix, for example raw deviations ("deviations") or deviation z-scores ("z") for a chromVAR deviations matrix.
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.