Description Usage Arguments Value
This function plots dimensionality reduction results and highlights cells based on known phenotype assignments
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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 |
Scatter plot of dimensionality reduction results
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