Heatmap: Heatmap

In bioinfoDZ/RISC: Robust Integration of Single-Cell RNA-Seq Datasets

Heatmap

Description

The "Heat" map makes heatmap to show gene expression patterns of single cells. The default groups cells into clusters, so the column of heatmap represents genes while the row of heatmap for the clusters of all the cells.

Usage

Heat(
  object,
  colFactor = NULL,
  genes = NULL,
  cells = NULL,
  gene.lab = FALSE,
  gene.cluster = 0,
  sample_bin = FALSE,
  ann_col = NULL,
  lim = NULL,
  smooth = "smooth",
  span = 0.75,
  degree = 1,
  palette = NULL,
  num = 50,
  con.bin = TRUE,
  cell.lab.size = 10,
  gene.lab.size = 5,
  value_only = FALSE,
  ...
)

Arguments

object	RISC object: a framework dataset.
colFactor	Use the factor (column name) in the coldata to make heatmap, but be factors.
genes	Use the gene expression values (gene symbol) to make heatmap, need to be inputted by the users.
cells	Use the subset cells of the whole coldata (cells) to make heatmap, the default is NULL and including all the cells.
gene.lab	Whether label gene names for the heatmap.
gene.cluster	The cluster numbers for gene clustering in the heatmap. The default is 0, without clustering genes.
sample_bin	The cell aggregating in samples, the default is FALSE.
ann_col	The annotation colors for colFactors, the input is a list.
lim	The gene expression range shown at heat-maps.
smooth	If use smooth to adjust heatmap, the default is "smooth" and another choice is "loess".
span	The loess span.
degree	The loess degree.
palette	The color palette used for heatmap. The default is brewer.pal(n = 7, name = "RdYlBu").
num	The cells for individual bin spans.
con.bin	Whether use consistent bin span.
cell.lab.size	The font size for column.
gene.lab.size	The font size for row.
value_only	Only return values.

References

Kolde, R. (2015)

Examples

# RISC object
obj0 = raw.mat[[3]]
gene0 = c('Gene718', 'Gene120', 'Gene313', 'Gene157', 'Gene30', 
          'Gene325', 'Gene415', 'Gene566', 'Gene990', 'Gene13', 
          'Gene604', 'Gene934', 'Gene231', 'Gene782', 'Gene10')
Heat(obj0, colFactor = 'Group', genes = gene0, gene.lab = TRUE, gene.cluster = 3, 
sample_bin = TRUE, lim = 2, gene.lab.size = 8)

bioinfoDZ/RISC documentation built on March 30, 2024, 9:19 p.m.