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)
#> 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