colorrepel (version 0.4.3)

average_clusters_rowwise: Rowwise math from matrix/data.frame per cluster based on another vector/metadata, similar to clustifyr::average_clusters but ids as rows

Description

Rowwise math from matrix/data.frame per cluster based on another vector/metadata, similar to clustifyr::average_clusters but ids as rows

Usage

average_clusters_rowwise(
  mat,
  metadata,
  cluster_col = "cluster",
  if_log = FALSE,
  cell_col = NULL,
  low_threshold = 0,
  method = "mean",
  output_log = FALSE,
  cut_n = NULL,
  trim = FALSE
)

Value

average expression matrix, with genes for row names, and clusters for column names

Arguments

mat

expression matrix

metadata

data.frame or vector containing cluster assignments per cell. Order must match column order in supplied matrix. If a data.frame provide the cluster_col parameters.

cluster_col

column in metadata with cluster number

if_log

input data is natural log, averaging will be done on unlogged data

cell_col

if provided, will reorder matrix first

low_threshold

option to remove clusters with too few cells

method

whether to take mean (default), median, 10% truncated mean, or trimean, max, min, sum

output_log

whether to report log results

cut_n

set on a limit of genes as expressed, lower ranked genes are set to 0, considered unexpressed

trim

whether to remove 1 percentile when doing min caluculation

Examples

mat <- average_clusters_rowwise(data.frame(
  y = c(1, 2, 3, 4, 5, 6),
  x = c(1, 2, 3, 4, 5, 6)
), metadata = c(1, 2, 1, 2, 1, 2), method = "min")