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

Description Usage Arguments Value

Description

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

Usage

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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.