plot_pseudotime_heatmap {monocle} | R Documentation

## Plots a pseudotime-ordered, row-centered heatmap

### 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).

[Package monocle version 2.22.0 Index]