heatmap: Renders a component containing a Heatmap.

In loosolab/i2dash.scrnaseq: Iterative and Interactive Dashboards for single-cell RNA-sequencing data

Description

Renders a component containing a Heatmap.

Usage

heatmap(dashboard, object, ...)

## S4 method for signature 'i2dashboard,missing'
heatmap(
  dashboard,
  exprs_values,
  split_by = NULL,
  aggregate_by = NULL,
  title = NULL,
  legend = NULL,
  cluster_rows = FALSE,
  cluster_columns = FALSE,
  show_column_names = FALSE,
  clustering_distance = c("euclidean", "maximum", "manhattan", "binary", "minkowski"),
  clustering_method = c("average", "ward.D", "ward.D2", "single", "complete",
    "mcquitty", "median", "centroid"),
  column_title = NULL,
  row_title = NULL,
  transmitter = NULL
)

## S4 method for signature 'i2dashboard,SingleCellExperiment'
heatmap(
  dashboard,
  object,
  exprs_values = "counts",
  subset_row = NULL,
  split_by = NULL,
  aggregate_by = NULL,
  ...
)

## S4 method for signature 'i2dashboard,Seurat'
heatmap(
  dashboard,
  object,
  assay = "RNA",
  assay_slot = "data",
  subset_row = NULL,
  split_by = NULL,
  aggregate_by = NULL,
  ...
)

Arguments

dashboard	An object of class i2dashboard.
object	A valid SingleCellExperiment object.
...	Further parameters passed to the core function.
exprs_values	A data.frame (matrix) containing expression data of features of interest in rows and samples in columns or a string representing the name of an assay of object.
split_by	An optional data.frame (matrix) containing grouping factors for spliting columns of the heatmap. In case of i2dashboard,SingleCellExperiment, should be column names of colData(object).
aggregate_by	An optional data.frame (matrix) containing grouping factors for aggregating columns of the heatmap. In case of i2dashboard,SingleCellExperiment, should be column names of colData(object).
title	Title of the component.
legend	Title of the heatmap legend.
cluster_rows	Whether or not to perform clustering on rows.
cluster_columns	Whether or not to perform clustering on columns
show_column_names	Whether or not to show column names. Note that large number of column names can cause visualization problems.
clustering_distance	The distance measure to use for hierarchical clustering.
clustering_method	Method to perform hierarchical clustering, passed to hclust.
column_title	The column title of the heatmap.
row_title	The row title of the heatmap.
transmitter	A character defining the id of an existing transmitter to obtain the data from.
subset_row	An optional character vector (of feature names), a logical vector or numeric vector (of indices) specifying the features to use. The default of NULL will use the first 100 features.
assay	A character specifying the assay (object@assays) to obtain expression values from. (Default: "RNA")
assay_slot	A character specifying the name of the data slot in the assay. (Default: "data")

Value

A string containing markdown code for the rendered component

loosolab/i2dash.scrnaseq documentation built on Jan. 1, 2021, 8:23 a.m.