# How to make a plot that groups different type of nodes by cluster? **URL:** \ **Category:** Usage\ **Tags:** R\ **Created:** [28 August 2020 22:02 UTC](https://igraph.discourse.group/t/how-to-make-a-plot-that-groups-different-type-of-nodes-by-cluster/425 "2020-08-28T22:02:55Z")\ **Posts on this page:** 4\ **Page:** 1
**Author:** ![Madhu](https://avatars.discourse-cdn.com/v4/letter/m/a8b319/32.png) [@Madhu](https://igraph.discourse.group/u/Madhu)\ **Post date:** [28 August 2020 22:02 UTC](https://igraph.discourse.group/t/how-to-make-a-plot-that-groups-different-type-of-nodes-by-cluster/425/1 "2020-08-28T22:02:55Z")
I have a dataframe `df` with nodes information like below: ``` dput(df) structure(list(Names = c("A4GALT", "AASS", "ABCA10", "ABCA7", "ABCD4", "ABHD4", "ABTB1", "AC006978.2", "AC009119.2"), type = c("typeA", "typeA", "typeC", "typeA", "typeC", "typeC", "typeB", "typeB", "typeB"), type_num = c(1L, 1L, 3L, 1L, 3L, 3L, 2L, 2L, 2L), Clusters = c("Cluster1", "Cluster1", "Cluster2", "Cluster3", "Cluster3", "Cluster1", "Cluster2", "Cluster3", "Cluster2")), row.names = c(NA, 9L), class = "data.frame") ``` So, in the `df` dataframe, there are 4 columns. `Names` is the gene name, `type` is different types A, B and C, `type_num` is the number given to each type and column `Clusters` show 3 clusters in which each gene belong to. Similarly, I have other dataframe `df2` with with edges information. And below I’m showing that: ``` dput(df2) structure(list(fromNode = c("A4GALT", "A4GALT", "A4GALT", "A4GALT", "A4GALT", "A4GALT", "A4GALT", "A4GALT", "AASS", "AASS", "AASS", "AASS", "AASS", "AASS", "AASS", "ABCA10", "ABCA10", "ABCA10", "ABCA10", "ABCA10", "ABCA10", "ABCA7", "ABCA7", "ABCA7", "ABCA7", "ABCA7", "ABCD4", "ABCD4", "ABCD4", "ABCD4", "ABHD4", "ABHD4", "ABHD4", "ABTB1", "ABTB1", "AC006978.2"), toNode = c("AASS", "ABCA10", "ABCA7", "ABCD4", "ABHD4", "ABTB1", "AC006978.2", "AC009119.2", "ABCA10", "ABCA7", "ABCD4", "ABHD4", "ABTB1", "AC006978.2", "AC009119.2", "ABCA7", "ABCD4", "ABHD4", "ABTB1", "AC006978.2", "AC009119.2", "ABCD4", "ABHD4", "ABTB1", "AC006978.2", "AC009119.2", "ABHD4", "ABTB1", "AC006978.2", "AC009119.2", "ABTB1", "AC006978.2", "AC009119.2", "AC006978.2", "AC009119.2", "AC009119.2"), weight = c(0.005842835, 0.002253695, 0.014513253, 0.004851739, 0.066702792, 0.009418991, 0.001136938, 0.000474221, 0.004405601, 0.000666001, 0.005625977, 0.0333554, 0.004666223, 0.000103131, 0.00026302, 0.004514819, 0.029632695, 0.001825839, 0.028379806, 0.001403298, 0.008339397, 0.02393394, 0.004782329, 0.024767355, 0.002986813, 0.00559471, 0.005961539, 0.064831874, 0.013023138, 0.027935729, 0.006618816, 0.001134219, 0.012798368, 0.007961242, 0.01640476, 0.007997743 ), direction = c("undirected", "undirected", "undirected", "undirected", "undirected", "undirected", "undirected", "undirected", "undirected", "undirected", "undirected", "undirected", "undirected", "undirected", "undirected", "undirected", "undirected", "undirected", "undirected", "undirected", "undirected", "undirected", "undirected", "undirected", "undirected", "undirected", "undirected", "undirected", "undirected", "undirected", "undirected", "undirected", "undirected", "undirected", "undirected", "undirected")), row.names = c(NA, -36L), class = "data.frame") ``` I wanted to create a network like below which represents the clusters with types having different colors in each cluster. It should look something like this: ![Screen Shot 2020-08-28 at 23.53.37](https://global.discourse-cdn.com/free1/uploads/igraph/original/1X/c196b9c5c4c6dac24b8723dcbcaa05112354e6af.jpeg) In the above image the numbers represent different clusters and colors represent different types which belong to each cluster and connected. Can anyone please help me how to create a network like above to collapse each cluster into a single network node and visualize a network with clusters as nodes. Any help is appreciated. thank you in advance. ---
**Author:** ![vtraag](https://yyz2.discourse-cdn.com/free1/user_avatar/igraph.discourse.group/vtraag/32/38_2.png) [@vtraag](https://igraph.discourse.group/u/vtraag)\ **Post date:** [25 September 2020 10:48 UTC](https://igraph.discourse.group/t/how-to-make-a-plot-that-groups-different-type-of-nodes-by-cluster/425/2 "2020-09-25T10:48:58Z")
To generate the network you can use [`graph_from_data_frame`](https://www.rdocumentation.org/packages/igraph/versions/1.2.5/topics/as_data_frame). You can cluster the graph with several different algorithms, e.g. using [`cluster_infomap`](https://www.rdocumentation.org/packages/igraph/versions/1.2.5/topics/cluster_infomap). You can collapse each cluster in a single network node by using [`contract`](https://www.rdocumentation.org/packages/igraph/versions/1.2.5/topics/contract). You can simply provide the [`membership`](https://www.rdocumentation.org/packages/igraph/versions/1.2.5/topics/membership) vector of the resulting clustering. You probably also want to simplify. ```auto H <- contract(G, membership(communities)) H <- simplify(H, remove.loops=FALSE) ``` You can then simply plot the resulting graph `H`. ---
**Author:** ![Madhu](https://avatars.discourse-cdn.com/v4/letter/m/a8b319/32.png) [@Madhu](https://igraph.discourse.group/u/Madhu)\ **Post date:** [25 September 2020 11:36 UTC](https://igraph.discourse.group/t/how-to-make-a-plot-that-groups-different-type-of-nodes-by-cluster/425/3 "2020-09-25T11:36:11Z")
Thank you for your reply. What is the object G here. Which data did you take? And I tried doing the network but it didn’t look good and I wanted to increase the distance between the clusters here [[How to increase the distance between the clusters using igraph?](https://igraph.discourse.group/t/how-to-increase-the-distance-between-the-clusters-using-igraph/459)] ---
**Author:** ![vtraag](https://yyz2.discourse-cdn.com/free1/user_avatar/igraph.discourse.group/vtraag/32/38_2.png) [@vtraag](https://igraph.discourse.group/u/vtraag)\ **Post date:** [25 September 2020 11:40 UTC](https://igraph.discourse.group/t/how-to-make-a-plot-that-groups-different-type-of-nodes-by-cluster/425/4 "2020-09-25T11:40:58Z")
> [@Madhu](#): > > What is the object G here. This is the graph object, please see the [documentation](https://www.rdocumentation.org/packages/igraph/versions/1.2.5/topics/contract). I have not used any data, this is just an example. You should construct the graph `G` yourself by using `graph_from_data_frame`, as said.