plot_genes_branched_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 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

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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.