generateUmapfromWSIR

A function to generate UMAP coordinates from the low-dimensional embedding of the gene expression data. These coordinates can later be plotted with the plotUmapFromWSIR function. Those two functions are separate so that you can generate the UMAP points only once using this function (which may take a long time), then modify the resulting plot as much as desired with the plotUmapFromWSIR function.

Usage

generateUmapFromWSIR(WSIR)

Arguments

WSIR

wsir object that is output of wSIR function. If you wish to generate UMAP plots based on other DR methods, ensure that the slot named "scores" in WSIR parameter contains the low-dimensional representation of exprs.

Value

matrix of UMAP coordinates of dimension nrow(coords) * 2. Output of this function can be directly used as the input to the plot_umap function.

Examples

data(MouseData)
wsir_obj = wSIR(X = sample1_exprs,
  coords = sample1_coords,
  optim_params = FALSE,
  alpha = 4,
  slices = 6) # create wsir object
umap_coords = generateUmapFromWSIR(WSIR = wsir_obj)
top_genes_obj = findTopGenes(WSIR = wsir_obj, highest = 4)
umap_plot = plotUmapFromWSIR(umap_coords = umap_coords,
  X = sample1_exprs,
  highest_genes = top_genes_obj,
  n_genes = 4)
umap_plot