geneADTnetwork {CiteFuse} | R Documentation

## geneADTnetwork

### Description

A function to visualise the features distribtuion

### Usage

    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)
    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)

[Package CiteFuse version 1.0.0 Index]