supercell_plot: Plot metacell NW

In SuperCell: Simplification of scRNA-Seq Data by Merging Together Similar Cells

Plot metacell NW

Description

Plot metacell NW

Usage

supercell_plot(
  SC.nw,
  group = NULL,
  color.use = NULL,
  lay.method = c("nicely", "fr", "components", "drl", "graphopt"),
  lay = NULL,
  alpha = 0,
  seed = 12345,
  main = NA,
  do.frames = TRUE,
  do.extra.log.rescale = FALSE,
  do.directed = FALSE,
  log.base = 2,
  do.extra.sqtr.rescale = FALSE,
  frame.color = "black",
  weights = NULL,
  min.cell.size = 0,
  return.meta = FALSE
)

Arguments

SC.nw	a super-cell (metacell) network (a field supercell_network of the output of SCimplify)
group	an assigment of metacells to any group (for ploting in different colors)
color.use	colros to use for groups, if NULL, an automatic palette of colors will be applied
lay.method	method to compute layout of the network (for the moment there several available: "nicely" for layout_nicely and "fr" for layout_with_fr, "components" for layout_components, "drl" for layout_with_drl, "graphopt" for layout_with_graphopt). If your dataset has clear clusters, use "components"
lay	a particular layout of a graph to plot (in is not NULL, lay.method is ignored and new layout is not computed)
alpha	a rotation of the layout (either provided or computed)
seed	a random seed used to compute graph layout
main	a title of a plot
do.frames	whether to keep vertex.frames in the plot
do.extra.log.rescale	whether to log-scale node size (to balance plot if some metacells are large and covers smaller metacells)
do.directed	whether to plot edge direction
log.base	base with thich to log-scale node size
do.extra.sqtr.rescale	whether to sqrt-scale node size (to balance plot if some metacells are large and covers smaller metacells)
frame.color	color of node frames, black by default
weights	edge weights used for some layout algorithms
min.cell.size	do not plot cells with smaller size
return.meta	whether to return all the meta data

Value

plot of a super-cell network

Examples

data(cell_lines) # list with GE - gene expression matrix (logcounts), meta - cell meta data
GE <- cell_lines$GE
cell.meta <- cell_lines$meta

SC <- SCimplify(GE,  # gene expression matrix
                gamma = 20) # graining level

# Assign metacell to a cell line
SC2cellline  <- supercell_assign(
    clusters = cell.meta, # single-cell assignment to cell lines
    supercell_membership = SC$membership) # single-cell assignment to metacells

# Plot metacell network colored by cell line
supercell_plot(SC$graph.supercells, # network
               group = SC2cellline, # group assignment
               main = "Metacell colored by cell line assignment",
               lay.method = 'nicely')

SuperCell documentation built on Oct. 25, 2024, 5:07 p.m.