plotTrajectoryHeatmap: Plot a Heatmap of Features across a Trajectory
In haibol2016/ArchR_debug: Analyzing single-cell regulatory chromatin in R.

plotTrajectoryHeatmap

R Documentation

Plot a Heatmap of Features across a Trajectory

Description

This function will plot a heatmap of the results from getTrajectory

Usage

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.