sc_dimred: Function for plotting dimensionality reduction results and...

In grant-duclos/scplots:

Description

This function plots dimensionality reduction results and highlights cells based on known phenotype assignments

Usage

sc_dimred(
  dataset = dataset,
  dimred = dimred,
  type = type,
  pheno.var = pheno.var,
  pheno.order = FALSE,
  pheno.colors = pheno.colors,
  pheno.var.2 = FALSE,
  pheno.var.2.target = pheno.var.2.target,
  ax.labels = TRUE,
  title = FALSE,
  size = 6
)

Arguments

dataset	ExpressionSet object
dimred	2-D output of t-SNE, UMAP, or PCA: Matrix with 2 columns corrersponding to dimensions 1 (x-axis) & 2 (y-axis), row numbers equivalent to the number of cells, and rownames corresponding to cell IDs
type	Options include "tsne", "umap", or "pca"
pheno.var	Character; Cells are highlighted according to specified phenotype variable
pheno.order	Logical or Character; FALSE if default order; Vector of pheno.var sub-groups to be plotted
pheno.colors	Character; Colors to highlight pheno.var sub-groups ordered according to pheno.order
pheno.var.2	Logical or Character; FALSE if no additional subsetting, otherwise specify secondary phenotype variable to subset from pheno.var pheno.order
pheno.var.2.target	Character; specify pheno.var.2 sub-group(s) to be visualized
ax.labels	Logical; RUE if x- and y-axis labeled according to specified type, FALSE if no axis labels
title	Logical or Character; FALSE if no title, otherwise specify title in quotes
size	Numeric; point size, default is 6

Value

Scatter plot of dimensionality reduction results

grant-duclos/scplots documentation built on July 26, 2020, 7:22 a.m.