CrossTalkeR Cookbook

James S. Nagai

Institute for Computational Genomics, Faculty of Medicine, RWTH Aachen University, Aachen, 52074 Germany

Vanessa Klöker

Institute for Computational Genomics, Faculty of Medicine, RWTH Aachen University, Aachen, 52074 Germany

Ivan G. Costa

Institute for Computational Genomics, Faculty of Medicine, RWTH Aachen University, Aachen, 52074 Germany

Version Info

suppressPackageStartupMessages({
  require(CrossTalkeR)
})
suppressPackageStartupMessages({
  require(igraph)
})
suppressPackageStartupMessages({
  require(ggraph)
})
suppressPackageStartupMessages({
  require(ggplot2)
})

R version: R version 4.4.1 (2024-06-14)

Package version: 1.4.2

Generate Report Example

In our vignette we provide examples on how to analyse cell interactions from a human myelofibrosis single cell RNA-seq dataset.

data(CTR)
data(EXP)
paths <- list('CTR'=CTR,
              'EXP'=EXP)

genes <- c('TGFB1|L')
output <- system.file("extdata", package = "CrossTalkeR")
data <- generate_report(paths,
                        genes,
                        out_path=file.path(output),
                        threshold=0,
                        out_file = 'vignettes_example.html',
                        output_fmt = "html_document",
                        report = TRUE)

Individual Visualization

CCI

plot_cci(
  graph = data@graphs$CTR,
  colors = data@colors,
  plt_name = "Example 1",
  coords = data@coords[V(data@graphs$CTR)$name, ],
  emax = NULL,
  leg = FALSE,
  low = 0,
  high = 0,
  ignore_alpha = FALSE,
  log = FALSE,
  efactor = 8,
  vfactor = 12
)

Sankey plot

plot_sankey(
  lrobj_tbl = data@tables$EXP_x_CTR,
  target = c("TGFB1|L"),
  ligand_cluster = NULL,
  receptor_cluster = NULL,
  plt_name = "TGFB1"
)

Report Samples

Single

Comparative

Session information