plot_heatmap: Plots a heatmap

In kgellatl/SignallingSingleCell: Network Analysis for single cell RNA sequencing Data (sc-RNASeq)

Description

Makes either a single cell or bulk heatmap,

Usage

plot_heatmap(
  input,
  genes,
  type,
  facet_by = FALSE,
  scale_group = F,
  title = "Heatmap",
  scale_by = "row",
  cluster_by = "row",
  cluster_type = "hierarchical",
  k = NULL,
  show_k = F,
  ceiling = FALSE,
  color_pal = viridis::magma(256),
  color_facets = FALSE,
  group_names = TRUE,
  gene_names = TRUE,
  text_angle = 90,
  pdf_format = "tile",
  interactive = FALSE,
  text_sizes = c(20, 10, 5, 10, 5, 5),
  gene_labels = NULL,
  gene_labels_size = 2,
  gene_labels_nudge = -0.5,
  gene_labels_col = 1,
  gene_labels_force = 1,
  return_results = F
)

Arguments

input	the input ex_sc
genes	a vector of genes to go into the heatmap
type	can either be "bulk" or "single_cell. If type is "bulk" it will utilize the bulk info stored in fData
facet_by	will create breaks in the heatmap by some pData Variable
title	A heatmap title
scale_by	scale across "row" (genes), "col" (groups), or FALSE
cluster_by	either "row", col, or both
cluster_type	"kmeans" or "hierarchical"
k	if cluster type is kmeans must provide k
ceiling	A value above which to truncate
color_pal	The color pallete to be used
color_facets	if true will use colors instead of text labels for the facets
group_names	whether groups should be labelled
gene_names	whether genes should be labelled
text_angle	The desired angle for text on the group labels
pdf_format	can be "tile" or "raster." tile is generally higher quality while raster is more efficient
text_sizes	a vector of title_size, axis_title, axis_text, legend_title, legend_text, facet_text, faults too c(20,10,5,10,5,5)
plotly	if true will be interactive # note that this option cannot be saved with save_ggplot(), and also is time consuming for single cell heatmaps

Details

Utilize information stored in pData to control the plot display.

Examples

plot_tsne_metadata(ex_sc_example, color_by = "UMI_sum", title = "UMI_sum across clusters", facet_by = "Cluster", ncol = 3)

kgellatl/SignallingSingleCell documentation built on Dec. 29, 2021, 4:12 p.m.