ReducedHeatmap: ReducedHeat

In milescsmith/ReducedHeat: Produces heatmap from a 1d dimensional reduction

Description

Compute Heatmap using dimensional reduction

Usage

ReducedHeatmap(object, ...)

## Default S3 method:
ReducedHeatmap(object, features, dim_embedding,
  cell_labels, enrich = 0, breaks = 100, slope = 50,
  intercept = 0.05, dendrogram = "row", titleX = FALSE,
  RowV = TRUE, show_legend = FALSE, hide_colorbar = FALSE,
  fontsize_row = 7, margins = c(70, 50, NA, 0), ...)

## S3 method for class 'Seurat'
ReducedHeatmap(object, assay = NULL, slot = "data",
  features = NULL, ident = NULL, reduction = "tsne", dimension = 1,
  ...)

## S3 method for class 'SingleCellExperiment'
ReducedHeatmap(object,
  assay = "logcounts", features = NULL, ident = NULL,
  reduction = "tsne", dimension = 1, ...)

Arguments

object	Object or expression matrix to visualize. Rownames should be gene names
...	Additional parameters to pass to heatmaply
features	Features to plot
dim_embedding	Cell embedding within the dimension of interest
cell_labels	Labels for each cell. While this is generally the cluster identity for a cell, it can be any discrete metadata variable
enrich	For every item in features, find a number of features equal to enrich that are close to that feature in the distance induced by the 1D UMAP
breaks	Number of bins
slope	For better visualization, transform the values with a logistic function. This is the slope of that function.
intercept	For better visualization, transform the values with a logistic function. This is the intercept of that function.
dendrogram	See heatmaply help. Default: "row"
titleX	See heatmaply help. Default: FALSE.
RowV	See heatmaply help. Default: TRUE
show_legend	See heatmaply help. Default: FALSE
hide_colorbar	See heatmaply help. Default: FALSE
fontsize_row	See heatmaply help. Default: 7
margins	See heatmaply help. Default: c(70, 50, NA, 0)
assay	Assay to use. Default: the object's current default assay.
slot	Slot to use. Default: "data"
ident	Object variable to use when determining cell_labels
reduction	Reduction to visualize. Default: 'umap'
dimension	The dimension to visualize. Default: 1

milescsmith/ReducedHeat documentation built on Feb. 22, 2020, 3:33 a.m.