View an initial object as a network

Translates the layout of the initial configuration object as a networks, representing panels as nodes and links between them as edges.

Usage

view_initial_network(initial, plot_format = c("igraph", "visNetwork", "none"))

Arguments

initial

An initial list object, in the format that is required to be passed as a parameter in the call to iSEE::iSEE().

plot_format

Character string, one of igraph, visNetwork, or none. Defaults to igraph. Determines the format of the visual representation generated as a side effect of this function - it can be the output of the plot() function for igraph objects, or an interactive widget created via visNetwork::visNetwork().

Value

An igraph object, underlying the visual representation provided.

Details

Panels are the nodes, with color and names to identify them easily. The connections among panels are represented through directed edges. This can be a compact visualization to obtain an overview for the configuration, without the need of fully launching the app and loading the content of all panels

This function is particularly useful with mid-to-large initial objects, as they can be quickly generated in a programmatic manner via the iSEEinit() provided in this package.

See also

view_initial_tiles()

Examples

## Load a dataset and preprocess this quickly
sce <- scRNAseq::RichardTCellData()
#> snapshotDate(): 2024-10-04
#> loading from cache
sce <- scuttle::logNormCounts(sce)
sce <- scater::runPCA(sce)
sce <- scater::runTSNE(sce)
## Select some features and aspects to focus on
gene_list <- c("ENSMUSG00000026581", "ENSMUSG00000005087", "ENSMUSG00000015437")
cluster <- "stimulus"
group <- "single cell quality"
initial <- iSEEinit(sce = sce,
                    features = gene_list,
                    clusters = cluster,
                    groups = group)

g_init <- view_initial_network(initial)

g_init
#> IGRAPH fe081a5 DN-- 13 4 -- 
#> + attr: name (v/c), color (v/c)
#> + edges from fe081a5 (vertex names):
#> [1] ReducedDimensionPlot1->ColumnDataPlot1  
#> [2] ReducedDimensionPlot2->ColumnDataPlot1  
#> [3] ReducedDimensionPlot3->ColumnDataPlot1  
#> [4] ReducedDimensionPlot4->FeatureAssayPlot4

view_initial_network(initial, plot_format = "visNetwork")
#> IGRAPH f8438ce DN-- 13 4 -- 
#> + attr: name (v/c), color (v/c)
#> + edges from f8438ce (vertex names):
#> [1] ReducedDimensionPlot1->ColumnDataPlot1  
#> [2] ReducedDimensionPlot2->ColumnDataPlot1  
#> [3] ReducedDimensionPlot3->ColumnDataPlot1  
#> [4] ReducedDimensionPlot4->FeatureAssayPlot4

## Continue your exploration directly within iSEE!
if (interactive())
  iSEE(sce, initial = initial)
#> Error in iSEE(sce, initial = initial): could not find function "iSEE"