Column graph plot

Source: R/AllClasses.R, R/class-ColumnGraphPlot.R

Network organisation for the samples of a SummarizedExperiment object. The igraph should be stored in the metadata slot by a name containing "graph". This panel uses plotColGraph to generate the plot.

Value

The ColumnGraphPlot(...) constructor creates an instance of a ColumnGraphPlot class, where any slot and its value can be passed to ... as a named argument.

Slot overview

This class inherits all slots from its parent class GraphPlot.

Author

Giulio Benedetti

Examples

library(mia)
library(miaViz)
#> Loading required package: ggplot2
#> Loading required package: ggraph
#> 
#> Attaching package: ‘miaViz’
#> The following object is masked from ‘package:mia’:
#> 
#>     plotNMDS
data("GlobalPatterns", library = "mia")
#> Warning: data set ‘mia’ not found
data("col_graph", library = "miaViz")
#> Warning: data set ‘miaViz’ not found

tse <- GlobalPatterns
tse <- agglomerateByRank(tse,
                         rank = "Genus",
                         na.rm = TRUE)
                         
metadata(tse)$graph <- col_graph

# Store panel into object
panel <- ColumnGraphPlot()
# View some adjustable parameters
head(slotNames(panel))
#> [1] "name"       "assay.type" "layout"     "edge.type"  "show.label"
#> [6] "add.legend"

# Launch iSEE with custom initial panel
if (interactive()) {
  iSEE(tse, initial = c(panel))
}