This function is a proxy to the PCA plot in comparative conditions

Usage

plot_pca_LR_comparative(
  lrobj_tblPCA,
  pca_table,
  dims = c(1, 2),
  ret = F,
  ggi = TRUE,
  include_tf = TRUE,
  gene_types = "all"
)

Arguments

lrobj_tblPCA: LRobject table with all data
pca_table: table entry
dims: PCA dims
ret: return plot
ggi: GGI mode
include_tf: intracellular option
gene_types: filter option of genes

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"
  )
)
output <- system.file("extdata", package = "CrossTalkeR")
genes <- c("TGFB1")

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