Plot t-SNE visualization of a data matrix

Usage

plot_tsne(
  data,
  labels,
  perplexity = 60,
  legend = "",
  plot.name = "",
  save = FALSE,
  rand.seed = 0,
  continuous = FALSE,
  labels2 = NULL,
  lim = NULL,
  runPCA = FALSE,
  alpha = 1
)

Arguments

data: The dxn matrix
labels: A vector of length n, usually cell clusters
perplexity: Perplexity value used for t-SNE
legend: A list of colors for the labels
plot.name: The plot title
save: If TRUE, save as plot.name.pdf
rand.seed: The random seed
continuous: Whether labels should be treated as continuous, e.g. pseudotime
labels2: Additional label
lim: Specify the xlim and y lim c(x_min, x_max, y_min, y_max)

Value

the figure if not save, otherwise save the figure as plot.name.pdf

Examples

results <- sim_example_200_cells()
#> Time spent: 0.01 mins
plot_tsne(log2(results$counts + 1), results$cell_meta$pop)