Plot Cell Cell Interaction — new_plot

This function do a CCI plot

Usage

new_plot_cci(
  graph,
  plt_name,
  emax = NULL,
  leg = FALSE,
  low = 25,
  high = 75,
  ignore_alpha = FALSE,
  log = FALSE,
  efactor = 8,
  vfactor = 12,
  vnames = TRUE,
  pg = NULL,
  vnamescol = NULL,
  colors,
  coords,
  col_pallet = NULL,
  standard_node_size = 20,
  pg_node_size_low = 10,
  pg_node_size_high = 60,
  arrow_size = 0.4,
  arrow_width = 0.8,
  node_label_position = 1.25,
  node_label_size = 0.6,
  score_filter = 0,
  cell_name_filter = NULL
)

Arguments

graph: Paths of single condition LR data
plt_name: Plot Name (Title)
emax: Max MeanLR across the all inputs, if its not defined, the method going to consider the max find within a sample
leg: Set color legend
low: Lower threshold: This parameter low and high defines the edges
high: Higher threshould which will be filtered. Edges within the interval [low\,high] are filtered.
ignore_alpha: not include transparency on the plot
log: logscale the interactions
efactor: edge scale factor
vfactor: edge scale factor
vnames: remove vertex labels
pg: pagerank values
colors: Cell type (Cluster) Colors
coords: object coordinates
col_pallet: Custom color pallet for the Edges
standard_node_size: Node size if no Pagerank values are given
pg_node_size_low: Smallest node size if Pagerank values are given
pg_node_size_high: Largest node size if Pagerank values are given
arrow_size: Scale value for the arrow size
arrow_width: Scale value for the arrow width
node_label_position: Scale Factor to move the node labels
node_label_size: Scale Factor to change the node label size
score_filter: Filter Graph by LR Score
cell_name_filter: Filter interactions by defined cell types

Value

R default plot

Examples

paths <- c(
  "CTR" = system.file("extdata",
    "CTR_LR.csv",
    package = "CrossTalkeR"
  ),
  "EXP" = system.file("extdata",
    "EXP_LR.csv",
    package = "CrossTalkeR"
  )
)

genes <- c("TGFB1")

output <- system.file("extdata", package = "CrossTalkeR")
data <- generate_report(paths,
  genes,
  out_path = paste0(output, "/"),
  threshold = 0,
  out_file = "vignettes_example.html",
  output_fmt = "html_document",
  report = FALSE
)
#> Warning: file("") only supports open = "w+" and open = "w+b": using the former
#> Error in read.table(file = file, header = header, sep = sep, quote = quote,     dec = dec, fill = fill, comment.char = comment.char, ...): no lines available in input
plot_cci(
  graph = data@graphs$CTR,
  colors = data@colors,
  plt_name = "Example 1",
  coords = data@coords[igraph::V(data@graphs$CTR)$name, ],
  emax = NULL,
  leg = FALSE,
  low = 0,
  high = 0,
  ignore_alpha = FALSE,
  log = FALSE,
  efactor = 8,
  vfactor = 12,
  vnames = TRUE
)
#> Error in data@graphs: no applicable method for `@` applied to an object of class "function"