readSubset: Sample data for plotting

In rliger: Linked Inference of Genomic Experimental Relationships

Sample data for plotting

Description

This function samples raw/normalized/scaled data from on-disk HDF5 files for plotting. This function assumes that the cell barcodes are unique across all datasets.

Usage

readSubset(
  object,
  slot.use = "norm.data",
  balance = NULL,
  max.cells = 1000,
  chunk = 1000,
  datasets.use = NULL,
  genes.use = NULL,
  rand.seed = 1,
  verbose = TRUE
)

Arguments

object	liger object. Should call normalize and selectGenes before calling.
slot.use	Type of data for sampling (raw.data, norm.data(default), scale.data).
balance	Type of sampling. NULL means that max_cells are sampled from among all cells; balance="dataset" samples up to max_cells from each dataset; balance="cluster" samples up to max_cells from each cluster.
max.cells	Total number of cell to sample (default 5000).
chunk	is the max number of cells at a time to read from disk (default 1000).
datasets.use	uses only the specified datasets for sampling. Default is NULL (all datasets)
genes.use	samples from only the specified genes. Default is NULL (all genes)
rand.seed	for reproducibility (default 1).
verbose	Print progress bar/messages (TRUE by default)

Value

liger object with sample.data slot set.

Examples

ligerex <- createLiger(list(ctrl = ctrl, stim = stim))
if (length(ligerex@H) > 0) {
    # Downsampling is calculated basing on factorization result
    ligerex <- readSubset(ligerex, slot.use = "norm.data", max.cells = 100)
}

rliger documentation built on Nov. 9, 2023, 1:07 a.m.