plot_heatmap_for_differential_genes: Plot heatmap for differential genes

In supatt-lab/SingCellaR: SingCellaR: an integrative analysis tool for single-cell RNA sequencing (scRNA-seq) data

Plot heatmap for differential genes

Description

Plot heatmap for differential genes

Usage

plot_heatmap_for_differential_genes(
  objectA = objectA,
  objectB = objectB,
  cellsA = c(),
  cellsB = c(),
  gene_list = c(),
  groupA.name = "",
  groupB.name = "",
  show.cell_annotation = c(),
  isClusterByRow = T,
  isClusterByCol = T,
  distance_row = "euclidean",
  distance_column = "euclidean",
  show_row_dend = T,
  show_column_dend = T,
  col.scaled.min = -2.5,
  col.scaled.max = 2.5,
  col.low = "blue",
  col.mid = "black",
  col.high = "red",
  rowFont.size = 6,
  use_raster = FALSE
)

Arguments

objectA	The SingCellaR objectA.
objectB	The SingCellaR objectB.
cellsA	The vector of cell names in group A.
cellsB	The vector of cell names in group B.
gene_list	The vector of gene names.
groupA.name	The group A cell names.
groupB.name	The group B cell names.
show.cell_annotation	The vector of cell annotation names
isClusterByRow	is logical. If TRUE, the clustering by row will be performed.
isClusterByCol	is logical. If TRUE, the clustering by column will be performed.
distance_row	The distance method for row. Default euclidean
distance_column	The distance method for column. Default euclidean
show_row_dend	is logical. If TRUE, the row dendrogram will be shown.
show_column_dend	is logical. If TRUE, the column dendrogram will be shown.
col.scaled.min	The minimum scaled value. Default -2.5
col.scaled.max	The maximum scaled value. Default 2.5
col.low	The low color gradient. Default blue
col.mid	The mid color gradient. Default black
col.high	The high color gradient. Default red
rowFont.size	The row font size. Default 6
use_raster	Whether render the heatmap body as a raster image. It helps to reduce file size when the matrix is huge.

supatt-lab/SingCellaR documentation built on Aug. 24, 2023, 5:49 p.m.