simple_xcell: Invoke xCell and pretty-ify the result.

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

Invoke xCell and pretty-ify the result.

Description

I initially thought xCell might prove the best tool/method for exploring cell deconvolution. I slowly figured out its limitations, but still think it seems pretty nifty for its use case. Thus this function is intended to make invoking it easier/faster.

Usage

simple_xcell(
  expt,
  signatures = NULL,
  genes = NULL,
  spill = NULL,
  expected_types = NULL,
  label_size = NULL,
  col_margin = 6,
  row_margin = 12,
  sig_cutoff = 0.2,
  verbose = TRUE,
  cores = 4,
  ...
)

Arguments

expt	Expressionset to query.
signatures	Alternate set of signatures to use.
genes	Subset of genes to query.
spill	The xCell spill parameter.
expected_types	Set of assumed types in the data.
label_size	How large to make labels when printing the final heatmap.
col_margin	Used by par() when printing the final heatmap.
row_margin	Ibid.
sig_cutoff	Only keep celltypes with a significance better than this.
verbose	Print some extra information during runtime.
cores	How many CPUs to use?
...	Extra arguments when normalizing the data for use with xCell.

Value

Small list providing the output from xCell, the set of signatures, and heatmap.

See Also

[xCell]

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.