Create a CellGraph object

Usage

CreateCellGraphObject(cellgraph, counts = NULL, layout = NULL, verbose = FALSE)

Arguments

cellgraph: A tbl_graph object representing an mpx single-cell graph
counts: A dgCMatrix with marker counts
layout: A tbl_df object with cell layout(s)
verbose: Print messages

Value

A CellGraph object

Examples


library(pixelatorR)
library(dplyr)
library(tidygraph)

edge_list <-
ReadMPX_item(
  system.file("extdata/five_cells",
              "five_cells.pxl",
              package = "pixelatorR"),
  items = "edgelist"
)
#> ℹ Loading item(s) from: /private/var/folders/gw/bdcqhnvs0m9gs_mq8n51jtbc0000gn/T/RtmpMJapOH/temp_libpatha88241f348a/pixelatorR/extdata/five_cells/five_cells.pxl
#> →   Loading edgelist data
#> ✔ Returning a 'tbl_df' object
bipart_graph <-
  edge_list %>%
  select(upia, upib, marker) %>%
  distinct() %>%
  as_tbl_graph(directed = FALSE) %>%
  mutate(node_type = case_when(name %in% edge_list$upia ~ "A", TRUE ~ "B"))
attr(bipart_graph, "type") <- "bipartite"

cg <- CreateCellGraphObject(cellgraph = bipart_graph)
cg
#> A CellGraph object containing a bipartite graph with 16800 nodes and 68255 edges