1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
|
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/plotting.R
\name{plot_pseudotime_heatmap}
\alias{plot_pseudotime_heatmap}
\title{Plots a pseudotime-ordered, row-centered heatmap}
\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{
\item{cds_subset}{CellDataSet for the experiment (normally only the branching genes detected with branchTest)}
\item{cluster_rows}{Whether to cluster the rows of the heatmap.}
\item{hclust_method}{The method used by pheatmap to perform hirearchical clustering of the rows.}
\item{num_clusters}{Number of clusters for the heatmap of branch genes}
\item{hmcols}{The color scheme for drawing the heatmap.}
\item{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.}
\item{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.}
\item{show_rownames}{Whether to show the names for each row in the table.}
\item{use_gene_short_name}{Whether to use the short names for each row. If FALSE, uses row IDs from the fData table.}
\item{norm_method}{Determines how to transform expression values prior to rendering}
\item{scale_max}{The maximum value (in standard deviations) to show in the heatmap. Values larger than this are set to the max.}
\item{scale_min}{The minimum value (in standard deviations) to show in the heatmap. Values smaller than this are set to the min.}
\item{trend_formula}{A formula string specifying the model used in fitting the spline curve for each gene/feature.}
\item{return_heatmap}{Whether to return the pheatmap object to the user.}
\item{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).
}
\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.
}
|
