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TomKellyGenetics avatar TomKellyGenetics commented on August 17, 2024

Sorry for the late response.

Here's an example, you can subset the data using the "igraph" package. Personally I use a custom plotting function plot_directed that I developed in R. You can install it on CRAN from the graphsim package. If you want to pass graph objects to other software such as Cytoscape I'm sure that igraph objects are supported for this:
http://cytoscape.org/RCy3/reference/createNetworkFromIgraph.html
https://www.bioconductor.org/packages/release/bioc/vignettes/RCy3/inst/doc/Cytoscape-and-iGraph.html

The resolution parameter depends on your cost function. It's documented in more detail in the Python version. Resolution profiling is not support in R currently.
https://leidenalg.readthedocs.io/en/stable/advanced.html?highlight=resolution#resolution-profile

library("leiden")
#> conda environment r-reticulate installed
#> python modules igraph and leidenalg installed
library("reticulate")
library("igraph")
#> 
#> Attaching package: 'igraph'
#> The following objects are masked from 'package:stats':
#> 
#>     decompose, spectrum
#> The following object is masked from 'package:base':
#> 
#>     union
set.seed(9000)
adj_mat <- matrix(round(runif(10000, 0, 1)), 100, 100)
snn_graph <- graph_from_adjacency_matrix(adj_mat)
partition <- leiden(snn_graph)
partition
#>   [1] 3 1 1 3 1 2 1 2 4 1 1 1 2 3 3 1 1 2 3 3 1 2 3 4 1 4 2 4 1 2 4 4 3 3 1 1 4
#>  [38] 2 4 1 2 1 1 2 2 1 2 3 2 3 2 2 1 2 2 1 3 3 3 1 2 1 3 1 2 3 4 2 3 2 4 4 1 3
#>  [75] 2 1 3 1 2 2 1 1 3 1 4 4 4 3 3 1 1 3 2 1 1 1 2 2 3 1
table(partition)
#> partition
#>  1  2  3  4 
#> 35 27 24 14
module_1 <- subgraph(snn_graph, V(snn_graph)[partition == 1])
#> Warning in subgraph(snn_graph, V(snn_graph)[partition == 1]): At
#> structural_properties.c:2051 :igraph_subgraph is deprecated from igraph 0.6, use
#> igraph_induced_subgraph instead
module_1 <- induced_subgraph(snn_graph, V(snn_graph)[partition == 1])
module_1
#> IGRAPH 1b6f683 D--- 35 710 -- 
#> + edges from 1b6f683:
#>   [1] 1-> 1 1-> 2 1-> 6 1-> 7 1-> 8 1-> 9 1->10 1->11 1->12 1->13 1->14 1->15
#>  [13] 1->18 1->19 1->20 1->23 1->25 1->26 1->28 1->29 1->32 2-> 1 2-> 3 2-> 4
#>  [25] 2-> 5 2-> 6 2-> 7 2-> 8 2->10 2->11 2->14 2->18 2->20 2->27 2->28 2->29
#>  [37] 2->32 2->33 2->34 2->35 3-> 2 3-> 3 3-> 4 3-> 5 3-> 8 3->10 3->14 3->16
#>  [49] 3->17 3->20 3->21 3->23 3->24 3->27 3->30 3->32 3->33 3->35 4-> 2 4-> 3
#>  [61] 4-> 4 4-> 5 4-> 6 4->11 4->12 4->13 4->15 4->16 4->17 4->18 4->19 4->27
#>  [73] 4->28 4->31 4->32 4->33 4->34 4->35 5-> 1 5-> 2 5-> 3 5-> 4 5-> 5 5-> 8
#>  [85] 5->10 5->11 5->12 5->14 5->17 5->19 5->25 5->26 5->29 5->30 5->31 5->33
#>  [97] 5->34 5->35 6-> 1 6-> 3 6-> 4 6-> 8 6->11 6->12 6->15 6->16 6->17 6->20
#> + ... omitted several edges
V(module_1)
#> + 35/35 vertices, from 1b6f683:
#>  [1]  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25
#> [26] 26 27 28 29 30 31 32 33 34 35
plot(module_1)

graphsim::plot_directed(module_1, cex.arrow = 0.75, cex.node = 1.5, col.arrow = "grey50", fill.node = "lightblue")

graphsim::plot_directed(snn_graph, cex.arrow = 0.75, cex.node = 1.5, col.arrow = "grey50",
                    fill.node = c("lightblue", "grey75")[ifelse(partition==1, 1, 2)])

Created on 2021-03-26 by the reprex package (v0.3.0)

from leiden.

EEmanetci avatar EEmanetci commented on August 17, 2024

thank you,
I will try this.

from leiden.

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