ssc.plot.heatmap: plot heatmap
In Japrin/sscVis: simpler single cell RNAseq data Visualization

ssc.plot.heatmap

R Documentation

plot heatmap

Description

plot heatmap

Usage

ssc.plot.heatmap(
  obj,
  assay.name = "exprs",
  out.prefix = NULL,
  ncell.downsample = NULL,
  ave.by = NULL,
  columns = NULL,
  columns.order = NULL,
  gene.desc = NULL,
  colSet = list(),
  pdf.width = 16,
  pdf.height = 15,
  do.scale = TRUE,
  z.lo = -2.5,
  z.hi = 2.5,
  z.step = 1,
  exp.title = "Exp",
  do.clustering.row = T,
  do.clustering.col = T,
  dend.col = FALSE,
  dend.row = FALSE,
  clustering.distance = "spearman",
  clustering.method = "complete",
  k.row = 1,
  k.col = 1,
  returnHT = FALSE,
  palette.name = NULL,
  palette.ann.numeric = "RdYlBu",
  Y.level.ann.numeric = NULL,
  row.split = NULL,
  column.split = NULL,
  annotation_legend_param = list(),
  ann.bar.height = 1.5,
  mytitle = "",
  ...
)

Arguments

`obj`	object of `SingleCellExperiment` class
`assay.name`	character; which assay (default: "exprs")
`out.prefix`	character; output prefix. (default: NULL)
`ncell.downsample`	integer; number of cells downsample to. (default: NULL)
`ave.by`	character; average the expression profile grouping by this. (default: NULL)
`columns`	character; columns in colData(obj) to be showd. must be subset of columns of colData(obj) and ave.by (if it's not NULL) (default: NULL)
`columns.order`	character; columns of colData(obj) used for ordering (default: NULL)
`gene.desc`	data.frame; it must contain columns geneID and Group (default: NULL)
`colSet`	list; mapping iterms in the names to colors in the values. (default: list())
`pdf.width`	double; width of the pdf file. (default:16)
`pdf.height`	double; height of the pdf file. (default:15)
`do.scale`	logical; wheter scale the rows, just for visualization. (default: TRUE)
`z.lo`	double; z-score lower boundary; z-score lower than this will be set to this (default: -2.5)
`z.hi`	double; z-score higher boundary; z-score higher than this will be set to this (default: 2.5)
`z.step`	double; z-score step, used for coloring the expression value (default: 1)
`exp.title`	character; title for the expression legend (default: "Exp")
`do.clustering.row`	logical; wheter order row (default: TRUE)
`do.clustering.col`	logical; wheter order columns (default: TRUE)
`dend.col`	dendrogram of the columns, 'cluster_columns' of ComplexHeatmap::Heatmap (default: FALSE)
`dend.row`	dendrogram of the rows, 'cluster_rows' of ComplexHeatmap::Heatmap (default: FALSE)
`clustering.distance`	character; one of spearmn, pearson, cosine and euclidean (default: "spearman")
`clustering.method`	character; method for hclust (default: "complete")
`k.row`	integer; number of clusters in the rows (default: 1)
`k.col`	integer; number of clusters in the columns (default: 1)
`returnHT`	logical; whether return HT; (default: FALSE)
`palette.name`	character; which palette to use, such as "RdBu","RdYlBu" (default: NULL)
`palette.ann.numeric`	character; which palette to use, such as "RdBu","RdYlBu" (default: "RdYlBu")
`Y.level.ann.numeric`	vector; value range for numeric annotation (default: NULL)
`row.split`	vector; used for row; must be named or is corresponding to the rows of obj (default: NULL)
`column.split`	vector; used for column; (default: NULL)
`annotation_legend_param`	list; (default: list())
`ann.bar.height`	double; height of the top annotation (default: 1.5)
`mytitle`	character; title of the figure (default: "")
`...`	parameters pass to plotMatrix.simple()