plot_heatmap: plot_heatmap

In dputhier/scigenex: The scigenex package (Single-Cell Informative GENe Explorer)

plot_heatmap

Description

Plot the observed and simulated distance with the Kth nearest neighbors.

Usage

plot_heatmap(
  object,
  center = TRUE,
  ceil = 1,
  floor = -1,
  cell_clusters = NULL,
  show_dendro = TRUE,
  use_top_genes = FALSE,
  interactive = TRUE,
  name = NULL,
  xlab = NULL,
  ylab = NULL,
  colorbar_name = "Exp. level",
  show_legend = TRUE,
  colors = colors_for_gradient("Ju1"),
  colors_cell_clusters = NULL,
  row_labels = TRUE,
  col_labels = FALSE,
  label_size = 10,
  line_size_vertical = 3,
  line_size_horizontal = 3,
  link = c("average", "complete", "single", "ward.D", "ward.D2", "mcquitty")
)

Arguments

object	A ClusterSet object.
center	A logical to indicate whether to center row..
ceil	A value for ceiling (NULL for no ceiling). Ceiling is performed centering.
floor	A value for flooring (NULL for no flooring). Flooring is performed after centering.
cell_clusters	A vector of cell clusters with cell barcodes as names.
show_dendro	A logical to indicate whether to show column dendrogram.
use_top_genes	A logical to indicate whether to use highly similar genes in the slot top_genes of ClusterSet.
interactive	A logical to indicate if the heatmap should be interactive.
name	A title for the heatmap (if interactive is TRUE).
xlab	A title for the x axis (if interactive is TRUE).
ylab	A title for the y axis (if interactive is TRUE).
colorbar_name	A title for the colorbar.
show_legend	A logical to indicate whether to show colorbar.
colors	A vector of colors.
colors_cell_clusters	A named vector of colors for cell identity annotations.
row_labels	A logical to indicate whether to show row labels.
col_labels	A logical to indicate whether to show col labels.
label_size	A value for label font size.
line_size_vertical	An integer for the size of horizontal white line which separate gene clusters.
line_size_horizontal	An integer for the size of vertical white line which separate cell clusters.
link	The aggloremative criterion for hierarchical clustering. One of "average", "complete" or "single". Default to average.

Value

Iheatmap-class object.

Examples

library(Seurat)
# Set verbosity to 1 to display info messages only.
set_verbosity(1)

# Load datasets
load_example_dataset('7871581/files/pbmc3k_medium_clusters')
load_example_dataset('7871581/files/pbmc3k_medium')

# Plot heatmap of 'top genes' of all gene clusters
pbmc3k_medium_clusters <- top_genes(pbmc3k_medium_clusters)
plot_heatmap(pbmc3k_medium_clusters, use_top_genes=TRUE)

# Plot heatmap of gene cluster 1
plot_heatmap(pbmc3k_medium_clusters[1,]) 

# Plot heatmap of gene cluster 1 and 3
plot_heatmap(pbmc3k_medium_clusters[c(1,3),])  

# Plot heatmap of 'top genes' of all gene clusters
# with cell ordered according to Seurat results
plot_heatmap(pbmc3k_medium_clusters, use_top_genes=TRUE, cell_clusters=Seurat::Idents(pbmc3k_medium))

# Plot heatmap of 'top genes' of all gene clusters
# with cell ordered according to Seurat results
# (non interactive version)
plot_heatmap(pbmc3k_medium_clusters, use_top_genes=TRUE, 
             cell_clusters=Seurat::Idents(pbmc3k_medium),
             interactive=FALSE, label_size = 2)

dputhier/scigenex documentation built on May 31, 2024, 8:59 a.m.