Description Usage Arguments References Examples
A plotting function to plot the inferred cell net-work from generateNetwork.
1 2 3 4 5 6 7 | plotCellNet(
net,
group = TRUE,
title = "Calculated Cell Network",
node_size = NULL,
show_select_by = "none"
)
|
net |
An igraph object generayed by generateNetwork. It contains the inferred cell-cell relationship. |
group |
A logical vector indicating whether to highlight cell communities in the network. If FALSE, they will not be highlighted. Default TRUE. |
title |
A character vector as the title of the network plot. |
node_size |
Size of node |
show_select_by |
Show option to highlight either by "node" or "group". Options: "node" | "group" | "none". Default "none". |
igraphscRGNet \insertRefvisNetworkscRGNet
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | # Example 1:
# Tested examples. Not run for fast package compiling
## Not run:
# Accessing the demo gene_counts_small dataset available with the package
inputCountsPath <- system.file("extdata", "GSE138852_small.csv", package = "scRGNet")
# Preprocess the raw counts
counts <- preprocessCSV(path = inputCountsPath)
ltmg <- runLTMG(counts)
hyperParams <- setHyperParams(regu_epochs = 5L)
hardwareSetup <- setHardware(coresUsage = 1L)
z <- runFeatureAE(scDataset = counts, LTMG_mat = ltmg, hyperParams, hardwareSetup)
net <- generateNetwork(z)
plotCellNet(net)
## End(Not run)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.