geneADTnetwork

A function to visualise the features distribtuion

geneADTnetwork(
  sce,
  RNA_exprs_value = "logcounts",
  altExp_name = "ADT",
  altExp_exprs_value = "logcounts",
  RNA_feature_subset = NULL,
  ADT_feature_subset = NULL,
  cell_subset = NULL,
  cor_threshold = 0.5,
  cor_method = c("pearson", "kendall", "spearman"),
  RNA_exprs_pct = 0.1,
  ADT_exprs_pct = 0.1,
  RNA_exprs_threshold = 0,
  ADT_exprs_threshold = 0,
  network_layout = NULL,
  return_igraph = FALSE
)

Arguments

sce	A singlecellexperiment object
RNA_exprs_value	A character indicates which expression value for RNA in assayNames is used.
altExp_name	A character indicates which expression matrix is used. by default is none (i.e. RNA).
altExp_exprs_value	A character indicates which expression value in assayNames is used.
RNA_feature_subset	A vector of characters indicates the subset of features of RNA that are used for visualisation
ADT_feature_subset	A vector of characters indicates the subset of features of ADT that are used for visualisation
cell_subset	A vector of characters indicates the subset of cells that are used for visualisation
cor_threshold	Thresholds of correlation.
cor_method	a character string indicating which correlation coefficient (or covariance) is to be computed. One of "pearson" (default), "kendall", or "spearman": can be abbreviated.
RNA_exprs_pct	A numeric indicates the threshold expression percentage of a gene to be considered in correlation analysis
ADT_exprs_pct	A numeric indicates the threshold expression percentage of a gene to be considered in correlation analysis
RNA_exprs_threshold	A numeric indicates the threshold of RNA expression. By default is 0.
ADT_exprs_threshold	A numeric indicates the threshold of ADT expression. By default is 0.
network_layout	layout of the network
return_igraph	indicates whether return the igraph object

Value

A igraph object of gene-ADT network

Examples

library(SingleCellExperiment)
#> Loading required package: SummarizedExperiment
#> Loading required package: GenomicRanges
#> Loading required package: IRanges
#> Loading required package: GenomeInfoDb
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> Loading required package: DelayedArray
#> Loading required package: matrixStats
#> 
#> Attaching package: ‘matrixStats’
#> The following objects are masked from ‘package:Biobase’:
#> 
#>     anyMissing, rowMedians
#> 
#> Attaching package: ‘DelayedArray’
#> The following objects are masked from ‘package:matrixStats’:
#> 
#>     colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
#> The following objects are masked from ‘package:base’:
#> 
#>     aperm, apply, rowsum
set.seed(2020)
data(sce_control_subset, package = "CiteFuse")
RNA_feature_subset <- sample(rownames(sce_control_subset), 50)
ADT_feature_subset <- rownames(altExp(sce_control_subset, "ADT"))

geneADTnetwork(sce_control_subset,
               RNA_feature_subset = RNA_feature_subset,
               ADT_feature_subset = ADT_feature_subset,
               cor_method = "pearson",
               network_layout = igraph::layout_with_fr)
#> IGRAPH ff83359 UN-B 2 1 -- 
#> + attr: name (v/c), label (v/c), class (v/c), type (v/l), shape (v/c),
#> | color (v/c), size (v/n), label.cex (v/n), label.color (v/c), value
#> | (e/n), color (e/c), weights (e/n)
#> + edge from ff83359 (vertex names):
#> [1] RNA_hg19_HCST--ADT_CD8