To visualize a given metacell partitioning by projecting metacells onto the single cell embedding space.

To visualize a given metacell partitioning by projecting metacells onto the single cell embedding space.

Usage

mcRigor_projection(
  obj_singlecell,
  sc_membership = NULL,
  sc.reduction = c("umap", "tsne", "pca"),
  dims = c(1, 2),
  metric = "size",
  add_testres = F,
  test_stats = NULL,
  Thre = NULL,
  test_cutoff = 0.01,
  color_field = NULL,
  cpalette = c("#13678A", "#45C4B0", "#9AEBA3", "#BF847E", "#F2C12E", "#7E57C2",
    "#FACFCE", "#9E9D24", "#DAFDBA", "#86ABD4", "#42A5F5", "#546E7A", "#D4E157",
    "#76FF03", "#6D4C41", "#004D40", "#AB47BC", "#D81B60"),
  sc.alpha = 0.5,
  mc.alpha = 1,
  pt_size = 1,
  axis_lab = F,
  max_mcsize = 1000,
  continuous_metric = T,
  dub_mc.label = F,
  dub_mc_test.label = F,
  label_text = F
)

Arguments

obj_singlecell

the Seurat object of single cells

sc_membership

A named vector (or dataframe) of the metacell membership of single cells

sc.reduction

The single cell reduction method to produce single cell embeddings

dims

The dimensions to use in the single cell embeddings

metric

The variable that determines the sizes of dots representing the metacells

add_testres

A bool indicating whether to add the mcRigor results (dubious or trustworthy) as part of obj_metacell's metadata

test_stats

If add_testres = True, this argument is needed. Usually should be TabMC, an output from previous steps.

Thre

The threshold for dubious metacell detection. If not inputed, it will be computed based on test_stats.

test_cutoff

The test size for dubious metacell detection testing

color_field

The variable based on which to color the cells.

cpalette

The color palette for visualization

sc.alpha

The level of single cell point transparency for visualization

mc.alpha

The level of metacell circle transparency for visualization

pt_size

The single cell point size for visualization

axis_lab

A bool indicating whether to add axis labels in visualization

max_mcsize

The maximum metacell size used for visualization scaling

continuous_metric

A bool indicating whether the field "metric" contains continuous values

dub_mc.label

A bool indicating whether to mark the ground truth dubious metacells using red color or not

dub_mc_test.label

A bool indicating whether to mark the detected dubious metacells using red color or not

label_text

A bool indicating whether to label the names of metacells or not

Value

a scatter plot of metacells projected to the single cell 2D embedding space.