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Plot Cell Cell Interaction

Source: R/plot.R
plot_cci.Rd

This function do a CCI plot

Usage

plot_cci(
  graph,
  colors,
  plt_name,
  coords,
  emax = NULL,
  leg = FALSE,
  low = 25,
  high = 75,
  ignore_alpha = FALSE,
  log = FALSE,
  efactor = 8,
  vfactor = 12,
  vnames = T,
  pg = NULL
)

Arguments

graph

Paths of single condition LR data

colors

Cell type (Cluster) Colors

plt_name

Plot Name (Title)

coords

object coordinates

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

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)
#> Create a Differential Table
#> Calculating CCI Ranking
#> EXP_x_CTR
#> 
#> Calculating GCI Ranking
#> EXP_x_CTR
#> Annotating the top Cell Genes
#> 'select()' returned 1:many mapping between keys and columns
#> 'select()' returned 1:many mapping between keys and columns
#> 'select()' returned 1:many mapping between keys and columns
#> 'select()' returned 1:many mapping between keys and columns
#> 'select()' returned 1:many mapping between keys and columns
#> 'select()' returned 1:many mapping between keys and columns
#> 'select()' returned 1:many mapping between keys and columns
#> 'select()' returned 1:many mapping between keys and columns
#> 'select()' returned 1:many mapping between keys and columns
#> 'select()' returned 1:many mapping between keys and columns
#> 'select()' returned 1:many mapping between keys and columns
#> 'select()' returned 1:many mapping between keys and columns
#> 'select()' returned 1:many mapping between keys and columns
#> 'select()' returned 1:many mapping between keys and columns
#> 'select()' returned 1:many mapping between keys and columns
#> 'select()' returned 1:many mapping between keys and columns
#> 'select()' returned 1:many mapping between keys and columns
#> 'select()' returned 1:many mapping between keys and columns
#> 'select()' returned 1:many mapping between keys and columns
#> 'select()' returned 1:many mapping between keys and columns
#> 'select()' returned 1:many mapping between keys and columns
#> 'select()' returned 1:many mapping between keys and columns
#> 'select()' returned 1:many mapping between keys and columns
#> 'select()' returned 1:many mapping between keys and columns
#> 'select()' returned 1:many mapping between keys and columns
#> 'select()' returned 1:many mapping between keys and columns
#> 'select()' returned 1:many mapping between keys and columns
#> 'select()' returned 1:many mapping between keys and columns
#> 'select()' returned 1:many mapping between keys and columns
#> 'select()' returned 1:many mapping between keys and columns
#> 'select()' returned 1:many mapping between keys and columns
#> 'select()' returned 1:many mapping between keys and columns
#> Adding missing grouping variables: `cellpair`
#> Adding missing grouping variables: `cellpair`
#> Network Analysis Done
#> Analysis Complete
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)