This function loads the single conditions LR outputs and return the LR network based analysis. It assumes that the table present the following columns ('source','target','gene_A','gene_B','type_gene_A','type_gene_B','MeanLR') measure
Usage
generate_report(
lrpaths,
genes = NULL,
tf_genes = NULL,
out_path,
sep = ",",
threshold = 0,
colors = NULL,
out_file = NULL,
report = TRUE,
output_fmt = "html_document",
sel_columns = c("source", "target", "gene_A", "gene_B", "type_gene_A", "type_gene_B",
"MeanLR"),
org = "hsa",
comparison = NULL,
filtered_net = F,
score_col = "LRScore"
)Arguments
- lrpaths
Paths of single condition LR data
- genes
list of genes to be considered in the sankey plots
- out_path
output directory path
- sep
character used on csv
- threshold
percentage of edges to be pruned
- colors
celltypes colorscheme
- out_file
output file names
- report
decide if a report is generated or not
- output_fmt
rmarkdown render output format parameter
- sel_columns
columns from data
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