plotmarkergenes: Plotting a Heatmap of Marker Gene Expression

Description

This functions generates a heatmap of expression for defined group of genes and can highlight the clustering partition and another sample grouping, e.g. origin or cell type.

Usage

plotmarkergenes(
  object,
  genes,
  imputed = FALSE,
  cthr = 0,
  cl = NULL,
  cells = NULL,
  order.cells = FALSE,
  aggr = FALSE,
  norm = FALSE,
  cap = NULL,
  flo = NULL,
  samples = NULL,
  cluster_cols = FALSE,
  cluster_rows = TRUE,
  cluster_set = FALSE,
  samples_col = NULL,
  zsc = FALSE,
  logscale = TRUE,
  noise = FALSE,
  fontsize = 10
)

Value

Object with clustering information for rows and columns returned by the function pheatmap from the package pheatmap.

Arguments

object: SCseq class object.
genes: A vector with a group of gene names corresponding to a subset of valid row names of the ndata slot of the SCseq object.
imputed: logical. If TRUE and imputing was done by calling compdist with knn > 0, then imputed expression values are shown. If FALSE, then raw counts are shown. Default is FALSE
cthr: Interger number greater or equal zero. Only clusters with >cthr cells are included in the t-SNE map. Default is 0.
cl: Vector of valid cluster numbers contained in slot cpart of the SCseq object. Default is NULL and all clusters with >cthr cells are included.
cells: Vector of valid cell names corresponding to column names of slot ndata of the SCseq object. Gene expression is only shown for this subset. Default is NULL and all cells are included. The set of cells is intersected with the subset of clusters in cl if given.
order.cells: logical. If TRUE, then columns of the heatmap are ordered by cell name and not by cluster number. If cells are given, then columns are ordered as in cells.
aggr: logical. If TRUE, then only average expression is shown for each cluster. Default is FALSE and expression in individual cells is shown.
norm: logical. If TRUE, then expression of each gene across clusters is normalized to 1, in order to depict all genes on the same scale. Default is FALSE.
cap: Numeric. Upper bound for gene expression. All values larger then cap are replaced by cap. Default is NULL and no cap is applied.
flo: Numeric. Lower bound for gene expression. All values smaller then flo are replaced by flo. Default is NULL and no flo is applied.
samples: A vector with a group of sample names for each cell in the same order as the column names of the ndata slot of the SCseq object.
cluster_cols: logical. If TRUE, then columns are clustered. Default is FALSE.
cluster_rows: logical. If TRUE, then rows are clustered. Default is TRUE.
cluster_set: logical. If TRUE then clusters are ordered by hierarchical clustering of the cluster medoids.
samples_col: Vector of colors used for highlighting all samples contained in samples in the heatmap. Default is NULL.
zsc: logical. If TRUE then a z-score transformation is applied. Default is FALSE.
logscale: logical. If TRUE then a log2 transformation is applied. Default is TRUE.
noise: logical. If TRUE then display local gene expression variability instead of gene expression (requires VarID analysis)/ Default value is FALSE.
fontsize: postive real number. Font size of gene name labels. Default is 10.