Visualize Gene t-SNE

Creates a t-SNE plot for visualizing gene partitions based on a given distance matrix.

VisualizeGeneTSNE(dist, gene_partition = NULL, filtered = TRUE)

Arguments

dist

matrix; a pairwise distance matrix of genes.

gene_partition

factor; a vector indicating the partition of genes into modules. Default is NULL.

filtered

logical; if TRUE, filters out some genes for each partition based on the SML method (Parisi et al., 2014). Default is TRUE.

Value

A ggplot2 object representing the t-SNE visualization of gene partitions.

References

Parisi, F., Strino, F., Nadler, B., & Kluger, Y. (2014). Ranking and combining multiple predictors without labeled data. Proceedings of the National Academy of Sciences, 111(4), 1253-1258. doi:10.1073/pnas.1219097111