plotHeatmap: Plots heatmap based on Celda model

In campbio/celda: CEllular Latent Dirichlet Allocation

Plots heatmap based on Celda model

Description

Renders a heatmap based on a matrix of counts where rows are features and columns are cells.

Usage

plotHeatmap(
  counts,
  z = NULL,
  y = NULL,
  scaleRow = scale,
  trim = c(-2, 2),
  featureIx = NULL,
  cellIx = NULL,
  clusterFeature = TRUE,
  clusterCell = TRUE,
  colorScheme = c("divergent", "sequential"),
  colorSchemeSymmetric = TRUE,
  colorSchemeCenter = 0,
  col = NULL,
  annotationCell = NULL,
  annotationFeature = NULL,
  annotationColor = NULL,
  breaks = NULL,
  legend = TRUE,
  annotationLegend = TRUE,
  annotationNamesFeature = TRUE,
  annotationNamesCell = TRUE,
  showNamesFeature = FALSE,
  showNamesCell = FALSE,
  rowGroupOrder = NULL,
  colGroupOrder = NULL,
  hclustMethod = "ward.D2",
  treeheightFeature = ifelse(clusterFeature, 50, 0),
  treeheightCell = ifelse(clusterCell, 50, 0),
  silent = FALSE,
  ...
)

Arguments

counts	Numeric or sparse matrix. Normalized counts matrix where rows represent features and columns represent cells. .
z	Numeric vector. Denotes cell population labels.
y	Numeric vector. Denotes feature module labels.
scaleRow	Function. A function to scale each individual row. Set to NULL to disable. Occurs after normalization and log transformation. Defualt is 'scale' and thus will Z-score transform each row.
trim	Numeric vector. Vector of length two that specifies the lower and upper bounds for the data. This threshold is applied after row scaling. Set to NULL to disable. Default c(-2,2).
featureIx	Integer vector. Select features for display in heatmap. If NULL, no subsetting will be performed. Default NULL.
cellIx	Integer vector. Select cells for display in heatmap. If NULL, no subsetting will be performed. Default NULL.
clusterFeature	Logical. Determines whether rows should be clustered. Default TRUE.
clusterCell	Logical. Determines whether columns should be clustered. Default TRUE.
colorScheme	Character. One of "divergent" or "sequential". A "divergent" scheme is best for highlighting relative data (denoted by 'colorSchemeCenter') such as gene expression data that has been normalized and centered. A "sequential" scheme is best for highlighting data that are ordered low to high such as raw counts or probabilities. Default "divergent".
colorSchemeSymmetric	Logical. When the colorScheme is "divergent" and the data contains both positive and negative numbers, TRUE indicates that the color scheme should be symmetric from [-max(abs(data)), max(abs(data))]. For example, if the data ranges goes from -1.5 to 2, then setting this to TRUE will force the color scheme to range from -2 to 2. Default TRUE.
colorSchemeCenter	Numeric. Indicates the center of a "divergent" colorScheme. Default 0.
col	Color for the heatmap.
annotationCell	Data frame. Additional annotations for each cell will be shown in the column color bars. The format of the data frame should be one row for each cell and one column for each annotation. Numeric variables will be displayed as continuous color bars and factors will be displayed as discrete color bars. Default NULL.
annotationFeature	A data frame for the feature annotations (rows).
annotationColor	List. Contains color scheme for all annotations. See '?pheatmap' for more details.
breaks	Numeric vector. A sequence of numbers that covers the range of values in the normalized 'counts'. Values in the normalized 'matrix' are assigned to each bin in 'breaks'. Each break is assigned to a unique color from 'col'. If NULL, then breaks are calculated automatically. Default NULL.
legend	Logical. Determines whether legend should be drawn. Default TRUE.
annotationLegend	Logical. Whether legend for all annotations should be drawn. Default TRUE.
annotationNamesFeature	Logical. Whether the names for features should be shown. Default TRUE.
annotationNamesCell	Logical. Whether the names for cells should be shown. Default TRUE.
showNamesFeature	Logical. Specifies if feature names should be shown. Default TRUE.
showNamesCell	Logical. Specifies if cell names should be shown. Default FALSE.
rowGroupOrder	Vector. Specifies the order of feature clusters when semisupervised clustering is performed on the y labels.
colGroupOrder	Vector. Specifies the order of cell clusters when semisupervised clustering is performed on the z labels.
hclustMethod	Character. Specifies the method to use for the 'hclust' function. See '?hclust' for possible values. Default "ward.D2".
treeheightFeature	Numeric. Width of the feature dendrogram. Set to 0 to disable plotting of this dendrogram. Default: if clusterFeature == TRUE, then treeheightFeature = 50, else treeheightFeature = 0.
treeheightCell	Numeric. Height of the cell dendrogram. Set to 0 to disable plotting of this dendrogram. Default: if clusterCell == TRUE, then treeheightCell = 50, else treeheightCell = 0.
silent	Logical. Whether to plot the heatmap.
...	Other arguments to be passed to underlying pheatmap function.

Value

list A list containing dendrogram information and the heatmap grob

Examples

data(celdaCGSim, celdaCGMod)
plotHeatmap(celdaCGSim$counts,
  z = celdaClusters(celdaCGMod)$z, y = celdaClusters(celdaCGMod)$y
)

campbio/celda documentation built on April 5, 2024, 11:47 a.m.