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") )
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.
The maximum number of features, ordered by variance, to consider from
A boolean value that indicates whether row-wise z-scores should be computed on the matrix provided by
A numeric vector of two numbers that represent the lower and upper limits of the heatmap color scheme.
A character vector or string that indicates the
A custom continuous palette (see
A character vector listing the
A number indicating how many of the top N features, based on variance, in
A boolean value that indicates whether all rows should be labeled on the side of the heatmap.
If wanting to set the order of rows to be plotted, the indices (integer or character correpsonding to rownmaes) can be provided here.
A character vector that indicates which
A boolean value that indicates whether the final heatmap matrix should be returned in lieu of plotting the actual heatmap.
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.
The path to a file to be used for logging ArchR output.