plot_pseudotime_heatmap: Plots a pseudotime-ordered, row-centered heatmap

In cole-trapnell-lab/monocle-release: Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq

Description

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.

Usage

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)

Arguments

cds_subset	CellDataSet for the experiment (normally only the branching genes detected with branchTest)
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.

Value

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).

cole-trapnell-lab/monocle-release documentation built on May 13, 2019, 8:50 p.m.