TrajectoryHeatmap.RdThis function generates a heatmap to visualize the data along inferred trajectory.
It was modified from the package ArchR plotTrajectoryHeatmap.
For more details, check here https://www.archrproject.com/reference/plotTrajectoryHeatmap.html.
TrajectoryHeatmap(
trajectory,
varCutOff = 0.9,
maxFeatures = 25000,
scaleRows = TRUE,
rowOrder = NULL,
limits = c(-1.5, 1.5),
labelRows = FALSE,
pal = NULL,
labelMarkers = NULL,
labelTop = 50,
name = "Heatmap",
returnMatrix = FALSE
)A SummarizedExperiment object that results from calling GetTrajectory
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 useMatrix when generating a trajectory
A boolean value that indicates whether row-wise z-scores should be computed on the matrix
If wanting to set the order of rows to be plotted, the indices (integer or character correpsonding to rownmaes) can be provided here.
A numeric vector of two numbers that represent the lower and upper limits of the heatmap color scheme.
A boolean value that indicates whether all rows should be labeled on the side of the heatmap.
A custom continuous palette used to override the default continuous palette for the heatmap.
A character vector listing the rownames that should be labeled on the side of the heatmap.
A number indicating how many of the top N features, based on variance of the matrix
Name of the matrix
A boolean value that indicates whether the final heatmap matrix should be returned in lieu of plotting the actual heatmap.
a heatmap