geneADTnetwork: geneADTnetwork

Description Usage Arguments Value Examples

View source: R/geneADTnetwork.R

Description

A function to visualise the features distribtuion

Usage

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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

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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)

CiteFuse documentation built on April 14, 2021, 6 p.m.