plot_pseudotime_heatmap: Plots a pseudotime-ordered, row-centered heatmap
In scfurl/m3addon: This package adds to the popular "monocle3"

Description Usage Arguments Value

The function plot_pseudotime_heatmap takes a CellDataSet object (usually containing a only subset of significant genes) and generates smooth expression curves much like plot_genes_in_pseudotime. Then, it clusters these genes and plots them using the pheatmap package. This allows you to visualize modules of genes that co-vary across pseudotime.

plot_pseudotime_heatmap(
  cds_subset,
  cluster_rows = TRUE,
  hclust_method = "ward.D2",
  num_clusters = 6,
  hmcols = NULL,
  add_annotation_row = NULL,
  add_annotation_col = NULL,
  show_rownames = FALSE,
  use_gene_short_name = TRUE,
  norm_method = c("log", "vstExprs"),
  scale_max = 3,
  scale_min = -3,
  trend_formula = "~sm.ns(Pseudotime, df=3)",
  return_heatmap = FALSE,
  cores = 1
)

`cds_subset`	CellDataSet for the experiment
`cluster_rows`	Whether to cluster the rows of the heatmap.
`hclust_method`	The method used by pheatmap to perform hirearchical clustering of the rows.
`num_clusters`	Number of clusters for the heatmap of branch genes
`hmcols`	The color scheme for drawing the heatmap.
`add_annotation_row`	Additional annotations to show for each row in the heatmap. Must be a dataframe with one row for each row in the fData table of cds_subset, with matching IDs.
`add_annotation_col`	Additional annotations to show for each column in the heatmap. Must be a dataframe with one row for each cell in the pData table of cds_subset, with matching IDs.
`show_rownames`	Whether to show the names for each row in the table.
`use_gene_short_name`	Whether to use the short names for each row. If FALSE, uses row IDs from the fData table.
`norm_method`	Determines how to transform expression values prior to rendering
`scale_max`	The maximum value (in standard deviations) to show in the heatmap. Values larger than this are set to the max.
`scale_min`	The minimum value (in standard deviations) to show in the heatmap. Values smaller than this are set to the min.
`trend_formula`	A formula string specifying the model used in fitting the spline curve for each gene/feature.
`return_heatmap`	Whether to return the pheatmap object to the user.
`cores`	Number of cores to use when smoothing the expression curves shown in the heatmap.

A list of heatmap_matrix (expression matrix for the branch committment), ph (pheatmap heatmap object), annotation_row (annotation data.frame for the row), annotation_col (annotation data.frame for the column).

scfurl/m3addon documentation built on Aug. 9, 2021, 5:30 p.m.