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

Description Usage Arguments Value

View source: R/swne_plotting.R

Description

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

Usage

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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 Dec. 7, 2018, 8:55 a.m.