plot_genes_branched_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 two branchs

@description returns a heatmap that shows changes in both lineages at the same time. It also requires that you choose a branch point to inspect. Columns are points in pseudotime, rows are genes, and the beginning of pseudotime is in the middle of the heatmap. As you read from the middle of the heatmap to the right, you are following one lineage through pseudotime. As you read left, the other. The genes are clustered hierarchically, so you can visualize modules of genes that have similar lineage-dependent expression patterns.

Usage

plot_genes_branched_heatmap(cds_subset, branch_point = 1,
  branch_states = NULL, branch_labels = c("Cell fate 1", "Cell fate 2"),
  cluster_rows = TRUE, hclust_method = "ward.D2", num_clusters = 6,
  hmcols = NULL, branch_colors = c("#979797", "#F05662", "#7990C8"),
  add_annotation_row = NULL, add_annotation_col = NULL,
  show_rownames = FALSE, use_gene_short_name = TRUE, scale_max = 3,
  scale_min = -3, norm_method = c("log", "vstExprs"),
  trend_formula = "~sm.ns(Pseudotime, df=3) * Branch",
  return_heatmap = FALSE, cores = 1, ...)

Arguments

cds_subset	CellDataSet for the experiment (normally only the branching genes detected with branchTest)
branch_point	The ID of the branch point to visualize. Can only be used when reduceDimension is called with method = "DDRTree".
branch_states	The two states to compare in the heatmap. Mutually exclusive with branch_point.
branch_labels	The labels for the branchs.
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.
branch_colors	The colors used in the annotation strip indicating the pre- and post-branch cells.
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.
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.
norm_method	Determines how to transform expression values prior to rendering
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.
...	Additional arguments passed to buildBranchCellDataSet

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.