PAGA abstracted graph over an embedding

Draws the PAGA graph with every cluster sitting at the centroid of its cells in an embedding, over a faint scatter of the cells themselves. A free layout of the abstracted graph puts the nodes somewhere arbitrary, which the reader then has to relate back to the embedding by hand. This does not.

The abstracted graph is close to complete on real data, so threshold is doing real work and dropping it to zero gives a hairball. tree_only is the shortcut to the backbone.

Usage

paga_plot_sc(
  object,
  paga_res,
  embedding = "umap",
  threshold = 0.01,
  tree_only = FALSE,
  node_colour_by = NULL,
  show_cells = TRUE,
  label = TRUE,
  embd_modality = c("rna", "adt", "wnn"),
  centroid = c("median", "mean"),
  point_size = NULL,
  point_alpha = 0.4,
  raster = NULL,
  raster_dpi = c(512, 512),
  cell_colour = "grey80",
  edge_colour = "grey40",
  edge_width = c(0.2, 3),
  max_node_size = 12,
  palette = NULL,
  label_size = 3,
  label_color = "black",
  label_font = "bold"
)

Arguments

object

A single cell class.

paga_res

PagaRes class. The output of bixverse::run_paga_sc(), run on this object.

embedding

String. Name of the embedding to position the nodes in.

threshold

Numeric. Edges below this connectivity are dropped (default: 0.01).

tree_only

Boolean. Draw the maximum spanning forest rather than the full abstracted graph (default: FALSE).

node_colour_by

Optional string. A numeric obs column summarised per cluster, e.g. "palantir_pseudotime", giving continuously coloured nodes. NULL (default) colours the nodes discretely by cluster.

show_cells

Boolean. Draw the cells underneath the graph (default: TRUE).

label

Boolean. Label the nodes with their cluster (default: TRUE).

embd_modality

String. One of c("rna", "adt", "wnn"). Modality the embedding is pulled from.

centroid

String. One of c("median", "mean"). How a cluster's position is summarised. Median by default, since embeddings throw stragglers that drag a mean off its cluster.

point_size

Optional numeric. Size of the cells. If not provided, will be auto-determined.

point_alpha

Numeric. Alpha of the cells (default: 0.4).

raster

Optional boolean. Shall the cell layer be rasterised. If NULL and the number of cells is larger than 1e5, defaults to TRUE.

raster_dpi

Two numerics. Pixel resolution for rasterized plots, passed to geom_scattermore(). Default is c(512, 512).

cell_colour

String. Colour of the cell layer (default: "grey80").

edge_colour

String. Colour of the edges (default: "grey40").

edge_width

Two numerics. Range the edge widths are scaled into (default: c(0.2, 3)).

max_node_size

Numeric. Size of the largest node. Node area tracks the cell count, which is what people read off it (default: 12).

palette

Optional string. Palette for the nodes, see bx_colors(). NULL (default) resolves to "main" for the discrete case and "sequential" when node_colour_by is given.

label_size

Numeric. Size of the labels.

label_color

String. Colour of the labels.

label_font

String. Font of the labels.

Value

A ggplot object.

References

Wolf, et al., Genome Biol., 2019.