Re: [R] igraph_vertex
On 2/24/24 12:10, Kimmo Elo wrote:
Hi,
first of all, your example was not reproducible! But once I added
"library(igraph)" and "library(scico)" plus generally replaced
"aes_collapsed" by "edge_list", I started to work :-)
After copying your lead in that replacement the error I got was:
network <- graph_from_data_frame(edge_list, directed= FALSE, + vertices
= details) #Error: object 'details' not found Same conclusion, though.
Incomplete presentation of code. -- David.
Anyway, the error is produced by this line:
+ edge.width= network,
It seems to me that you have forgotten to name a variable here (you now
use the whole network object as variable, which most probably won't
work).
Just as a kind advice for the future: if you encounter errors like
this, it is always a good idea to debug the problematic code by
commenting it out line by line. So you will - most probably - find our
those sections resulting in errors.
HTH,
Kimmo
la, 2024-02-24 kello 12:09 +0100, SIBYLLE STÖCKLI via R-help kirjoitti:
Dear R-community
It would be nice to get some input how to find a solution for the
following
error in igraph and vertex setting.
Thank you very much
Sibylle
par(bg="black")
network %>% plot(
+ vertex.color=clrs[V(.)$community],
+ vertex.size=V(.)$hub_score*1,
+ vertex.frame.color=V(.)$color,
+ vertex.label.color="white",
+ vertex.label.cex=0.5,
+ vertex.label.family="Helvetica",
+ vertex.label.font=1,
+ edge.curved=0.5,
+ edge.width= network,
+ layout=layout_with_mds(.))
Error in intI(i, n = x@Dim[1], dn[[1]], give.dn = FALSE) :
Index gr��er als maximales 6
Reproducible example:
edge_list<-read.csv("edges_table_Test.csv")
#create network and add some necessary attributes (vertices) for the
plot
network <- graph_from_data_frame(aes_collapsed, directed= FALSE,
vertices = details)
temp<-cluster_optimal(network)
temp<-cbind(membership=temp$membership, Names=temp$name)
aes_collapsed <- aes_collapsed %>%
merge(temp, by="Names")
network <- network %>%
set_edge_attr(name = "type", value = factor(aes_collapsed$Names,
ordered =
is.ordered(V(network)$name))) %>%
set_edge_attr(name = "membership", value =
aes_collapsed$membership) %>%
set_edge_attr(name = "color",
value = c(viridis::viridis(5))
[match(E(.)$type, c(factor(V(.)$name)))]) %>%
set_vertex_attr(name = "trans_v_net", value = c(transitivity(.,
type =
"local"))) %>%
set_vertex_attr(name = "hub_score", value = c(hub_score(.)$vector))
%>%
set_vertex_attr(name = "color",
value = c(viridis::viridis((5)))
[match(V(.)$name, c(factor(V(.)$name)))]) %>%
set_vertex_attr(name= "community",
value=cluster_optimal(.)$membership)
clrs<-scico(3, palette = "batlow")
par(bg="black")
network %>% plot(
vertex.color=clrs[V(.)$community],
vertex.size=V(.)$hub_score*5,
vertex.frame.color=V(.)$color,
vertex.label.color="white",
vertex.label.cex=0.5,
vertex.label.family="Helvetica",
vertex.label.font=1,
edge.curved=0.5,
edge.width= network,
layout=layout_with_mds(.))
edges_table_Test.csv
Names
target
weight
B.B
A.A
4
C.C
A.A
5
D.D
A.A
5
E.E
A.A
5
F.F
A.A
1
C.C
B.B
5
E.E
B.B
1
F.F
B.B
2
A.A
C.C
5
B.B
C.C
1
D.D
C.C
5
E.E
C.C
5
F.F
C.C
3
A.A
D.D
5
B.B
D.D
1
C.C
D.D
5
E.E
D.D
5
F.F
D.D
4
A.A
E.E
5
B.B
E.E
1
C.C
E.E
4
D.D
E.E
5
F.F
E.E
5
A.A
F.F
5
B.B
F.F
1
C.C
F.F
2
D.D
F.F
3
E.E
F.F
4
F.F
F.F
5
[[alternative HTML version deleted]]
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] igraph_vertex
Hi,
first of all, your example was not reproducible! But once I added
"library(igraph)" and "library(scico)" plus generally replaced
"aes_collapsed" by "edge_list", I started to work :-)
Anyway, the error is produced by this line:
+ edge.width= network,
It seems to me that you have forgotten to name a variable here (you now
use the whole network object as variable, which most probably won't
work).
Just as a kind advice for the future: if you encounter errors like
this, it is always a good idea to debug the problematic code by
commenting it out line by line. So you will - most probably - find our
those sections resulting in errors.
HTH,
Kimmo
la, 2024-02-24 kello 12:09 +0100, SIBYLLE STÖCKLI via R-help kirjoitti:
> Dear R-community
>
>
>
> It would be nice to get some input how to find a solution for the
> following
> error in igraph and vertex setting.
>
>
>
> Thank you very much
>
> Sibylle
>
>
>
> > par(bg="black")
>
> > network %>% plot(
>
> + vertex.color=clrs[V(.)$community],
>
> + vertex.size=V(.)$hub_score*1,
>
> + vertex.frame.color=V(.)$color,
>
> + vertex.label.color="white",
>
> + vertex.label.cex=0.5,
>
> + vertex.label.family="Helvetica",
>
> + vertex.label.font=1,
>
> + edge.curved=0.5,
>
> + edge.width= network,
>
> + layout=layout_with_mds(.))
>
> Error in intI(i, n = x@Dim[1], dn[[1]], give.dn = FALSE) :
>
> Index gr��er als maximales 6
>
>
>
>
>
> Reproducible example:
>
>
>
> edge_list<-read.csv("edges_table_Test.csv")
>
>
>
> #create network and add some necessary attributes (vertices) for the
> plot
>
> network <- graph_from_data_frame(aes_collapsed, directed= FALSE,
>
> vertices = details)
>
>
>
>
>
> temp<-cluster_optimal(network)
>
> temp<-cbind(membership=temp$membership, Names=temp$name)
>
> aes_collapsed <- aes_collapsed %>%
>
> merge(temp, by="Names")
>
>
>
>
>
> network <- network %>%
>
> set_edge_attr(name = "type", value = factor(aes_collapsed$Names,
>
> ordered =
> is.ordered(V(network)$name))) %>%
>
> set_edge_attr(name = "membership", value =
> aes_collapsed$membership) %>%
>
> set_edge_attr(name = "color",
>
> value = c(viridis::viridis(5))
>
> [match(E(.)$type, c(factor(V(.)$name)))]) %>%
>
> set_vertex_attr(name = "trans_v_net", value = c(transitivity(.,
> type =
> "local"))) %>%
>
> set_vertex_attr(name = "hub_score", value = c(hub_score(.)$vector))
> %>%
>
> set_vertex_attr(name = "color",
>
> value = c(viridis::viridis((5)))
>
> [match(V(.)$name, c(factor(V(.)$name)))]) %>%
>
> set_vertex_attr(name= "community",
> value=cluster_optimal(.)$membership)
>
>
>
> clrs<-scico(3, palette = "batlow")
>
>
>
> par(bg="black")
>
> network %>% plot(
>
> vertex.color=clrs[V(.)$community],
>
> vertex.size=V(.)$hub_score*5,
>
> vertex.frame.color=V(.)$color,
>
> vertex.label.color="white",
>
> vertex.label.cex=0.5,
>
> vertex.label.family="Helvetica",
>
> vertex.label.font=1,
>
> edge.curved=0.5,
>
> edge.width= network,
>
> layout=layout_with_mds(.))
>
>
>
>
>
> edges_table_Test.csv
>
>
>
>
> Names
>
> target
>
> weight
>
>
> B.B
>
> A.A
>
> 4
>
>
> C.C
>
> A.A
>
> 5
>
>
> D.D
>
> A.A
>
> 5
>
>
> E.E
>
> A.A
>
> 5
>
>
> F.F
>
> A.A
>
> 1
>
>
> C.C
>
> B.B
>
> 5
>
>
> E.E
>
> B.B
>
> 1
>
>
> F.F
>
> B.B
>
> 2
>
>
> A.A
>
> C.C
>
> 5
>
>
> B.B
>
> C.C
>
> 1
>
>
> D.D
>
> C.C
>
> 5
>
>
> E.E
>
> C.C
>
> 5
>
>
> F.F
>
> C.C
>
> 3
>
>
> A.A
>
> D.D
>
> 5
>
>
> B.B
>
> D.D
>
> 1
>
>
> C.C
>
> D.D
>
> 5
>
>
> E.E
>
> D.D
>
> 5
>
>
> F.F
>
> D.D
>
> 4
>
>
> A.A
>
> E.E
>
> 5
>
>
> B.B
>
> E.E
>
> 1
>
>
> C.C
>
> E.E
>
> 4
>
>
> D.D
>
> E.E
>
> 5
>
>
> F.F
>
> E.E
>
> 5
>
>
> A.A
>
> F.F
>
> 5
>
>
> B.B
>
> F.F
>
> 1
>
>
> C.C
>
> F.F
>
> 2
>
>
> D.D
>
> F.F
>
> 3
>
>
> E.E
>
> F.F
>
> 4
>
>
> F.F
>
> F.F
>
> 5
>
>
>
>
> [[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] igraph_vertex
Dear R-community
It would be nice to get some input how to find a solution for the following
error in igraph and vertex setting.
Error in intI(i, n = x@Dim[1], dn[[1]], give.dn = FALSE) :
Index größer als maximales 6
Kind regards
Sibylle
Working example
library(circlize)
library(ggplot2)
library(igraph)
library(tidyverse)
library(RColorBrewer)
library(stringi)
library(scico)
library(plotly)
library(ggraph)
edges_table_Test.csv
Names target weight
B.B A.A 4
C.C A.A 5
D.D A.A 5
E.E A.A 5
F.F A.A 1
C.C B.B 5
E.E B.B 1
F.F B.B 2
A.A C.C 5
B.B C.C 1
D.D C.C 5
E.E C.C 5
F.F C.C 3
A.A D.D 5
B.B D.D 1
C.C D.D 5
E.E D.D 5
F.F D.D 4
A.A E.E 5
B.B E.E 1
C.C E.E 4
D.D E.E 5
F.F E.E 5
A.A F.F 5
B.B F.F 1
C.C F.F 2
D.D F.F 3
E.E F.F 4
F.F F.F 5
edge_list<-read.csv("edges_table_Test.csv")
network <- graph_from_data_frame(aes_collapsed, directed= FALSE,
vertices = details)
temp<-cluster_optimal(network)
temp<-cbind(membership=temp$membership, Names=temp$name)
aes_collapsed <- aes_collapsed %>%
merge(temp, by="Names")
network <- network %>%
set_edge_attr(name = "type", value = factor(aes_collapsed$Names,
ordered =
is.ordered(V(network)$name))) %>%
set_edge_attr(name = "membership", value = aes_collapsed$membership) %>%
set_edge_attr(name = "color",
value = c(viridis::viridis(5))
[match(E(.)$type, c(factor(V(.)$name)))]) %>%
set_vertex_attr(name = "trans_v_net", value = c(transitivity(., type =
"local"))) %>%
set_vertex_attr(name = "hub_score", value = c(hub_score(.)$vector)) %>%
set_vertex_attr(name = "color",
value = c(viridis::viridis((5)))
[match(V(.)$name, c(factor(V(.)$name)))]) %>%
set_vertex_attr(name= "community", value=cluster_optimal(.)$membership)
clrs<-scico(3, palette = "batlow")
par(bg="black")
network %>% plot(
vertex.color=clrs[V(.)$community],
vertex.size=V(.)$hub_score*5,
vertex.frame.color=V(.)$color,
vertex.label.color="white",
vertex.label.cex=0.5,
vertex.label.family="Helvetica",
vertex.label.font=1,
edge.curved=0.5,
edge.width= network,
layout=layout_with_mds(.))
Error in intI(i, n = x@Dim[1], dn[[1]], give.dn = FALSE) :
Index größer als maximales 6
tiff("figures/AES_network_bymembership.tiff", width=1000, height=700, res=120)
network %>%
ggraph(., layout = "auto")+
geom_edge_arc(curvature=0.3, aes(width=(E(network)$weight/10), color=from,
alpha=0.5)) +
geom_node_point(aes(size = V(network)$hub_score*200, color=
as.factor(V(network)$community))) +
geom_node_text(aes(label = V(network)$name), size=5, color="white", repel=T)+
scale_color_scico_d(palette = "batlow")+
scale_edge_width(range = c(0.2,4))+
scale_size(range = c(0.5,20)) +
#scale_edge_color_manual(values = c(scico(21, palette="batlow")))+
theme(plot.background = element_rect(fill = "black"),
legend.position = "right",
panel.background = element_rect(fill = "black"))
dev.off()
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] igraph_vertex
The reason html is specifically advised against as a format is that it
does things like mangling data such as is happening in your example. You
should repost using settings on you mail client for plain-text. Your
code should start by loading necessary packages. You should also not
post screen output versions of code since that will insert lots of
superfluous "+"'s. Some but not all API will be able to strip those
characters.
--
David.
On 2/24/24 03:09, SIBYLLE STÖCKLI via R-help wrote:
Dear R-community
It would be nice to get some input how to find a solution for the following
error in igraph and vertex setting.
Thank you very much
Sibylle
par(bg="black")
network %>% plot(
+ vertex.color=clrs[V(.)$community],
+ vertex.size=V(.)$hub_score*1,
+ vertex.frame.color=V(.)$color,
+ vertex.label.color="white",
+ vertex.label.cex=0.5,
+ vertex.label.family="Helvetica",
+ vertex.label.font=1,
+ edge.curved=0.5,
+ edge.width= network,
+ layout=layout_with_mds(.))
Error in intI(i, n = x@Dim[1], dn[[1]], give.dn = FALSE) :
Index gr��er als maximales 6
Reproducible example:
edge_list<-read.csv("edges_table_Test.csv")
#create network and add some necessary attributes (vertices) for the plot
network <- graph_from_data_frame(aes_collapsed, directed= FALSE,
vertices = details)
temp<-cluster_optimal(network)
temp<-cbind(membership=temp$membership, Names=temp$name)
aes_collapsed <- aes_collapsed %>%
merge(temp, by="Names")
network <- network %>%
set_edge_attr(name = "type", value = factor(aes_collapsed$Names,
ordered =
is.ordered(V(network)$name))) %>%
set_edge_attr(name = "membership", value = aes_collapsed$membership) %>%
set_edge_attr(name = "color",
value = c(viridis::viridis(5))
[match(E(.)$type, c(factor(V(.)$name)))]) %>%
set_vertex_attr(name = "trans_v_net", value = c(transitivity(., type =
"local"))) %>%
set_vertex_attr(name = "hub_score", value = c(hub_score(.)$vector)) %>%
set_vertex_attr(name = "color",
value = c(viridis::viridis((5)))
[match(V(.)$name, c(factor(V(.)$name)))]) %>%
set_vertex_attr(name= "community", value=cluster_optimal(.)$membership)
clrs<-scico(3, palette = "batlow")
par(bg="black")
network %>% plot(
vertex.color=clrs[V(.)$community],
vertex.size=V(.)$hub_score*5,
vertex.frame.color=V(.)$color,
vertex.label.color="white",
vertex.label.cex=0.5,
vertex.label.family="Helvetica",
vertex.label.font=1,
edge.curved=0.5,
edge.width= network,
layout=layout_with_mds(.))
edges_table_Test.csv
Names
target
weight
B.B
A.A
4
C.C
A.A
5
D.D
A.A
5
E.E
A.A
5
F.F
A.A
1
C.C
B.B
5
E.E
B.B
1
F.F
B.B
2
A.A
C.C
5
B.B
C.C
1
D.D
C.C
5
E.E
C.C
5
F.F
C.C
3
A.A
D.D
5
B.B
D.D
1
C.C
D.D
5
E.E
D.D
5
F.F
D.D
4
A.A
E.E
5
B.B
E.E
1
C.C
E.E
4
D.D
E.E
5
F.F
E.E
5
A.A
F.F
5
B.B
F.F
1
C.C
F.F
2
D.D
F.F
3
E.E
F.F
4
F.F
F.F
5
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] igraph_vertex
Dear R-community
It would be nice to get some input how to find a solution for the following
error in igraph and vertex setting.
Thank you very much
Sibylle
> par(bg="black")
> network %>% plot(
+ vertex.color=clrs[V(.)$community],
+ vertex.size=V(.)$hub_score*1,
+ vertex.frame.color=V(.)$color,
+ vertex.label.color="white",
+ vertex.label.cex=0.5,
+ vertex.label.family="Helvetica",
+ vertex.label.font=1,
+ edge.curved=0.5,
+ edge.width= network,
+ layout=layout_with_mds(.))
Error in intI(i, n = x@Dim[1], dn[[1]], give.dn = FALSE) :
Index gr��er als maximales 6
Reproducible example:
edge_list<-read.csv("edges_table_Test.csv")
#create network and add some necessary attributes (vertices) for the plot
network <- graph_from_data_frame(aes_collapsed, directed= FALSE,
vertices = details)
temp<-cluster_optimal(network)
temp<-cbind(membership=temp$membership, Names=temp$name)
aes_collapsed <- aes_collapsed %>%
merge(temp, by="Names")
network <- network %>%
set_edge_attr(name = "type", value = factor(aes_collapsed$Names,
ordered =
is.ordered(V(network)$name))) %>%
set_edge_attr(name = "membership", value = aes_collapsed$membership) %>%
set_edge_attr(name = "color",
value = c(viridis::viridis(5))
[match(E(.)$type, c(factor(V(.)$name)))]) %>%
set_vertex_attr(name = "trans_v_net", value = c(transitivity(., type =
"local"))) %>%
set_vertex_attr(name = "hub_score", value = c(hub_score(.)$vector)) %>%
set_vertex_attr(name = "color",
value = c(viridis::viridis((5)))
[match(V(.)$name, c(factor(V(.)$name)))]) %>%
set_vertex_attr(name= "community", value=cluster_optimal(.)$membership)
clrs<-scico(3, palette = "batlow")
par(bg="black")
network %>% plot(
vertex.color=clrs[V(.)$community],
vertex.size=V(.)$hub_score*5,
vertex.frame.color=V(.)$color,
vertex.label.color="white",
vertex.label.cex=0.5,
vertex.label.family="Helvetica",
vertex.label.font=1,
edge.curved=0.5,
edge.width= network,
layout=layout_with_mds(.))
edges_table_Test.csv
Names
target
weight
B.B
A.A
4
C.C
A.A
5
D.D
A.A
5
E.E
A.A
5
F.F
A.A
1
C.C
B.B
5
E.E
B.B
1
F.F
B.B
2
A.A
C.C
5
B.B
C.C
1
D.D
C.C
5
E.E
C.C
5
F.F
C.C
3
A.A
D.D
5
B.B
D.D
1
C.C
D.D
5
E.E
D.D
5
F.F
D.D
4
A.A
E.E
5
B.B
E.E
1
C.C
E.E
4
D.D
E.E
5
F.F
E.E
5
A.A
F.F
5
B.B
F.F
1
C.C
F.F
2
D.D
F.F
3
E.E
F.F
4
F.F
F.F
5
[[alternative HTML version deleted]]
__
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