Generate a report for given LRObj

Generate a report for given LRObj

Usage

make_report(
  genes = NULL,
  tf_genes = NULL,
  out_path,
  threshold = 0,
  colors = NULL,
  out_file = NULL,
  output_fmt = "html_document",
  LRObj = NULL,
  sel_columns = c("source", "target", "gene_A", "gene_B", "type_gene_A", "type_gene_B",
    "MeanLR")
)

Arguments

genes

list of genes to be considered in the sankey plots

out_path

output directory path

threshold

percentage of edges to be pruned

colors

celltypes colorscheme

out_file

output file names

output_fmt

rmarkdown render output format parameter

LRObj

rmarkdown render output format parameter

sel_columns

columns from data

Value

Rmarkdown report all objects from each step

Examples

paths <- c('CTR' = system.file("extdata",
                              "CTR_LR.csv",
                              package = "CrossTalkeR"),
          'EXP' = system.file("extdata",
                              "EXP_LR.csv",
                              package = "CrossTalkeR"))
output =  system.file("extdata", package = "CrossTalkeR")
genes <- c('TGFB1')
data <- generate_report(lrpaths = paths,
                       genes = genes,
                       out_path = paste0(output,'/'),
                       threshold = 0,
                         out_file = "report.html")
#> 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