Weird variable names from edgeBuild() #18
Description
Hello,
I am trying to generate networks using your ggClusterNet R package. I am having a hard time understanding why I have some my OTUs name appearing into the headers of the resulted edge object. Please see below.
> rare_ggclust_net2 <- ggClusterNet::model_igraph(cor = cor_rare,
+ method = "cluster_fast_greedy",
+ seed = 12,
+ Top_M = 20)
> str(rare_ggclust_net2)
List of 3
$ :'data.frame': 300 obs. of 3 variables:
..$ X1 : num [1:300] 1.59 4.89 -6.97 -5.49 9.54 ...
..$ X2 : num [1:300] 1.4 5.79 8.32 7.07 1.36 ...
..$ elements: chr [1:300] "OTU_1" "OTU_2" "OTU_3" "OTU_1835" ...
$ :'data.frame': 300 obs. of 6 variables:
..$ orig_model: num [1:300] 7 8 9 10 11 3 1 12 13 14 ...
..$ model : chr [1:300] "model_7" "model_8" "model_9" "model_10" ...
..$ color : chr [1:300] "#FDB567" "#FDD07D" "#FEE695" "#FEF6B1" ...
..$ OTU : chr [1:300] "OTU_1" "OTU_2" "OTU_3" "OTU_1835" ...
..$ X1 : num [1:300] 1.59 4.89 -6.97 -5.49 9.54 ...
..$ X2 : num [1:300] 1.4 5.79 8.32 7.07 1.36 ...
$ :Class 'igraph' hidden list of 10
..$ : num 300
..$ : logi FALSE
..$ : num [1:7973] 0 1 2 3 4 5 17 6 20 30 ...
..$ : num [1:7973] 0 1 2 3 4 5 5 6 6 6 ...
..$ : NULL
..$ : NULL
..$ : NULL
..$ : NULL
..$ :List of 4
.. ..$ : num [1:3] 1 0 1
.. ..$ : Named list()
.. ..$ :List of 5
.. .. ..$ name : chr [1:300] "OTU_1" "OTU_2" "OTU_3" "OTU_1835" ...
.. .. ..$ modularity : num [1:300] 7 8 9 10 11 3 1 12 13 14 ...
.. .. ..$ label : logi [1:300] NA NA NA NA NA NA ...
.. .. ..$ color : chr [1:300] "#FDB567" "#FDD07D" "#FEE695" "#FEF6B1" ...
.. .. ..$ frame.color: chr [1:300] "#FDB567" "#FDD07D" "#FEE695" "#FEF6B1" ...
.. ..$ :List of 3
.. .. ..$ weight : num [1:7973] 1 1 1 1 1 ...
.. .. ..$ correlation: num [1:7973] 1 1 1 1 1 ...
.. .. ..$ color : chr [1:7973] "#FDB567" "#FDD07D" "#FEE695" "#FEF6B1" ...
..$ :<environment: 0x559d09955508>
Then I generate nodes
> node_rare <-
+ rare_ggclust_net2[[1]]
> head(node_rare)
X1 X2 elements
OTU_1 1.585925 1.398903 OTU_1
OTU_2 4.890295 5.793571 OTU_2
OTU_3 -6.967662 8.316252 OTU_3
OTU_1835 -5.494072 7.068775 OTU_1835
OTU_5 9.542700 1.359537 OTU_5
OTU_4 -8.606428 6.845587 OTU_4
I generate the taxonomy
> taxonomy_rare <-
+ physeq_rare_net %>%
+ vegan_tax() %>%
+ as.data.frame()
> head(taxonomy_rare)
Kingdom Phylum Class Order Family Genus Species
OTU_1 Eukaryota Streptophyta Magnoliopsida Poales Poaceae Setaria Setaria viridis
OTU_2 Eukaryota Streptophyta Magnoliopsida <NA> <NA> <NA> <NA>
OTU_3 Eukaryota Streptophyta Magnoliopsida Malpighiales Euphorbiaceae <NA> <NA>
OTU_1835 Eukaryota Streptophyta Magnoliopsida Poales Poaceae <NA> <NA>
OTU_5 Eukaryota Streptophyta Magnoliopsida Asterales Asteraceae <NA> <NA>
OTU_4 Eukaryota Ascomycota Dothideomycetes Pleosporales Phaeosphaeriaceae Parastagonospora Parastagonospora nodorum
I add taxonomy and mean abundance to the nodes
> nodes_net = nodeadd(plotcord = node_rare,
+ otu_table = otutable_rare,
+ tax_table = taxonomy_rare)
> head(nodes_net)
X1 X2 elements Kingdom Phylum Class Order Family Genus Species mean
OTU_1 1.585925 1.3989030 OTU_1 Eukaryota Streptophyta Magnoliopsida Poales Poaceae Setaria Setaria viridis 8574.82245
OTU_10 -6.163169 -9.7805123 OTU_10 Eukaryota Streptophyta Magnoliopsida Poales Poaceae Digitaria Digitaria exilis 244.55310
OTU_100 8.443559 -3.5408620 OTU_100 Eukaryota Basidiomycota Pucciniomycetes Pucciniales Pucciniaceae <NA> <NA> 12.24806
OTU_101 11.854691 -2.6231469 OTU_101 Eukaryota Basidiomycota Agaricomycetes Agaricales <NA> <NA> <NA> 10.77710
OTU_102 9.114853 -0.1619759 OTU_102 Eukaryota Arthropoda Arachnida Sarcoptiformes <NA> <NA> <NA> 18.45071
OTU_103 7.771214 -6.5407734 OTU_103 Eukaryota Basidiomycota Ustilaginomycetes Ustilaginales Ustilaginaceae <NA> <NA> 18.22406
And finally I generate the edglist that strangely give me some weird names as HEADER... Why OTU_1 and OTU_2 are considered variable names instead of variable labels?
> edges_net <-
+ ggClusterNet::edgeBuild(cor = cor_rare,
+ node = node_rare) %>%
+ dplyr::select(-cor) %>% # not sure why cor did not work
+ mutate(direction = if_else(weight > 0, "positive", "negative"))
> head(edges_net)
X2 Y2 OTU_2 OTU_1 weight X1 Y1 direction
1 -8.606428 6.845587 OTU_4 OTU_124 0.8019252 -9.302795 5.740050 positive
2 -5.988042 -11.696418 OTU_839 OTU_3669 0.8489268 -5.500506 -10.835631 positive
3 -5.988042 -11.696418 OTU_839 OTU_2406 0.8079077 -5.611176 -10.502029 positive
4 -5.988042 -11.696418 OTU_839 OTU_1930 0.8513364 -5.644883 -10.621819 positive
5 -5.988042 -11.696418 OTU_839 OTU_1192 0.8057194 -5.117171 -9.954975 positive
6 -5.988042 -11.696418 OTU_839 OTU_3167 0.8315849 -5.087309 -10.538837 positive
>
Additionally when I use the any of the ploygon layout methods I got a weird output when the variable cor is repeaded twice with values that make no sense (e.g. -) or placed in the same place as the Order level. Please see below.
> rare_ggclust_net2 <- ggClusterNet::PolygonClusterG(cor = cor_rare,
+ nodeGroup = net_rare)
> # Generate nodes
> node_rare <-
+ rare_ggclust_net2[[1]]
> # Generate taxonomy
> taxonomy_rare <-
+ physeq_rare_net %>%
+ vegan_tax() %>%
+ as.data.frame()
> # Add taxonomy, mean abundance to nodes
> nodes_net = nodeadd(plotcord = node_rare,
+ otu_table = otutable_rare,
+ tax_table = taxonomy_rare)
> edges_net <-
+ ggClusterNet::edgeBuild(cor = cor_rare,
+ node = nodes_net)
> head(edges_net)
X2 Y2 OTU_2 Kingdom.x Phylum.x Class.x Order.x cor Genus.x Species.x mean.x OTU_1 weight X1 Y1 Kingdom.y Phylum.y
1 0.6237351 17.93444 OTU_10 Eukaryota Streptophyta Magnoliopsida Poales Poaceae Digitaria Digitaria exilis 244.5531 OTU_3669 -0.8406234 1.220210 17.740636 Bacteria Pseudomonadota
2 0.6237351 17.93444 OTU_10 Eukaryota Streptophyta Magnoliopsida Poales Poaceae Digitaria Digitaria exilis 244.5531 OTU_2406 -0.8567855 1.763356 17.427051 Bacteria Pseudomonadota
3 0.6237351 17.93444 OTU_10 Eukaryota Streptophyta Magnoliopsida Poales Poaceae Digitaria Digitaria exilis 244.5531 OTU_1930 -0.8368905 16.033626 -2.194569 Bacteria Pseudomonadota
4 0.6237351 17.93444 OTU_10 Eukaryota Streptophyta Magnoliopsida Poales Poaceae Digitaria Digitaria exilis 244.5531 OTU_2272 -0.8183972 11.042347 14.145455 Bacteria Pseudomonadota
5 0.6237351 17.93444 OTU_10 Eukaryota Streptophyta Magnoliopsida Poales Poaceae Digitaria Digitaria exilis 244.5531 OTU_1192 -0.8025917 16.492326 6.651734 Eukaryota <NA>
6 0.6237351 17.93444 OTU_10 Eukaryota Streptophyta Magnoliopsida Poales Poaceae Digitaria Digitaria exilis 244.5531 OTU_2356 -0.8153681 -12.026043 -2.659660 Bacteria Verrucomicrobiota
Class.y Order.y Family.y Genus.y Species.y mean.y cor
1 Deltaproteobacteria Myxococcales Kofleriaceae Haliangium uncultured bacterium 133.78123 -
2 Alphaproteobacteria Hyphomicrobiales <NA> <NA> <NA> 98.46497 -
3 Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas uncultured bacterium 91.78690 -
4 Alphaproteobacteria Hyphomicrobiales Nitrobacteraceae Bradyrhizobium <NA> 67.04703 -
5 <NA> <NA> <NA> <NA> <NA> 66.33284 -
6 Spartobacteria <NA> <NA> <NA> <NA> 62.33723 -
Thanks for your help,
Gian