Error in toVisNetworkData(g) : igraph must be a igraph object

umerijaz / microbiomeSeq

An R package for microbial community analysis in an environmental context

66 stars 26 forks source link

Error in toVisNetworkData(g) : igraph must be a igraph object #46

Open nbutyrate opened 4 years ago

nbutyrate commented 4 years ago

i am trying to run "co_occurence_network". But there id no graph creation i.e.

g <- co_occr$net$graph NULL

following is the workflow

co_occr <- co_occurence_network(physeq, grouping_column = "AllPos", rhos = c("-0.5", "0.5"),

method = "cor", qval_threshold = 0.05, select.condition = "Yes", scale.vertex.size = 4,
scale.edge.width = 10)
```
g <- co_occr$net$graph
```
data <- toVisNetworkData(g) Error in toVisNetworkData(g) : igraph must be a igraph object g NULL co_occr $net $net$edgelists pairs trt taxa1 taxa2 1 Lichtheimia Fusarium Yes Lichtheimia Fusarium 2 Aspergillus Cystofilobasidium Yes Aspergillus Cystofilobasidium

svenyos commented 4 years ago

I have the same problem. The graph object in the output from co_occurence_network() is NULL

cherrypashka commented 3 years ago

Hi! I have the same problem, even on pitlatrine data from example. data(pitlatrine) physeq <- taxa_level(pitlatrine, "Phylum") co_occr <- co_occurence_network(physeq, grouping_column = "Country", rhos = 0.35, scale.vertex.size=3, scale.edge.width=15) g <- co_occr$net$graph print(g) NULL data <- toVisNetworkData(g) visNetwork(nodes = data$nodes, edges = data$edges, width = 900, height = 900) %>% visOptions(highlightNearest = TRUE, nodesIdSelection = TRUE)

Error in toVisNetworkData(g) : igraph must be a igraph object

passdan commented 3 years ago

From the future, also having the same issue. Wondering if anyone else managed to solve?

gdanetzk commented 2 years ago

Even further in the future, same issue. Anyone solve it?