SuperCell (version 1.0)

supercell_plot: 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
)

Value

plot of a super-cell network

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

Examples

# \donttest{
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')
# }