plot_multiple_branches_heatmap: Create a heatmap to demonstrate the bifurcation of gene...

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

Description

Create a heatmap to demonstrate the bifurcation of gene expression along multiple branches

Usage

plot_multiple_branches_heatmap(cds, branches, branches_name = NULL,
  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("vstExprs", "log"), scale_max = 3, scale_min = -3,
  trend_formula = "~sm.ns(Pseudotime, df=3)", return_heatmap = FALSE,
  cores = 1)

Arguments

cds	CellDataSet for the experiment (normally only the branching genes detected with BEAM)
branches	The terminal branches (states) on the developmental tree you want to investigate.
branches_name	Name (for example, cell type) of branches you believe the cells on the branches are associated with.
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.