average_clusters_rowwise {colorrepel}R Documentation

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
)

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

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

Value

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

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")

[Package colorrepel version 0.1.0 Index]