plotTrajectoryHeatmap.Rd
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 |
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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. |