custom_feature_plot: Make tSNE plots (or PCA, or Monocle; it's customizable)
In maehrlab/thymusatlastools: Tools for analysis of single-cell transcriptomic data

Make tSNE plots (or PCA, or Monocle; it's customizable)

custom_feature_plot(dge, colour = NULL, subset_id = NULL,
  axes = c("tSNE_1", "tSNE_2"), fix_coords = T, show_axes = F,
  alpha = 1, cols.use = c("khaki1", "red"), use_rank = F,
  overplot_adjust = F)

`dge`	Seurat object
`colour`	Variable to fetch and plot. Length-1 character. "plain_grey" returns a dark grey plot.
`subset_id`	Vector of subsets to include on the plot. Cells not included will still be included via geom_blank so as to preserve the scale of the plot.
`axes`	Variables to fetch for use on X and Y axes. Defaults to tSNE embedding.
`fix_coords`	Force the plot to be square? Defaults to T, because a rotated or reflected version of the tSNE embedding should convey the exact same relationships.
`alpha`	Transparency. Number between 0 and 1.
`cols.use`	Colorscale. Character vector, hexadecimal or e.g. c("khaki1", "red"). For discrete data fetched for "colour", should be named with the variable's levels.
`use_rank`	Transform expression level to ranks before plotting?
`overplot_adjust`	Bin points within hexagons. Nice for Monocle embeddings.