CheckGeneEmbedding: Validates gene embeddings by plotting cluster logFC vs gene...

In yanwu2014/swne: Similarity Weighted Nonnegative Embedding: A method for visualizing high dimensional datasets

Validates gene embeddings by plotting cluster logFC vs gene factor loading logFC Warns users if embedded genes fall below minimum logFC threshold

Description

Validates gene embeddings by plotting cluster logFC vs gene factor loading logFC Warns users if embedded genes fall below minimum logFC threshold

Usage

CheckGeneEmbedding(
  W,
  norm.counts,
  genes.embed,
  sample.groups,
  n.bins = 50,
  min.cluster.logfc = 1.5,
  min.factor.logfc = 1.5,
  font.size = 12,
  label.size = 5,
  eps = 1e-04
)

Arguments

W	Gene loadings matrix
norm.counts	Normalized gene expression matrix
genes.embed	Genes to embed onto SWNE plot
sample.groups	Sample groupings
n.bins	Number of bins for the hexbin plot
min.cluster.logfc	Minimum cluster logFC for an embedded gene
min.factor.logfc	Minimum factor logFC for an embedded gene
font.size	Axis label font size
label.size	Gene label size
eps	Pseudocount to add to fold-change calculations

Value

Dataframe with cluster logFC and factor logFC. Generates scatterplot as a side effect.

yanwu2014/swne documentation built on Aug. 5, 2023, 4:42 a.m.