Re: [R] igraph_vertex
В Mon, 26 Feb 2024 11:52:13 +0100 пишет: > TIFFOpen: figures/AES_network_bymembership.tiff: Cannot open. > Warning message: > In dev.off() : > unable to open TIFF file 'figures/AES_network_bymembership.tiff' In the current directory (see getwd()), is there a subdirectory named "figures"? Do you have write access to this subdirectory? Is there a file named "AES_network_bymembership.tiff" in the subdirectory named "figures"? Could it be open by a different program and therefore locked? Unfortunately, libtiff doesn't seem to provide any more information regarding why it couldn't open the file at this point. -- Best regards, Ivan __ 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 Ivan
Thanks a lot.
I used:
windowsFonts(Helvetica = windowsFont("Helvetica"))
No warning now with Helvetica
Additionally I used "sans", similarly no warning in the first part.
But still not able to open tiff with both versions:
Using "stress" as default layout
> dev.off()
TIFFOpen: figures/AES_network_bymembership.tiff: Cannot open.
RStudioGD
2
Warning message:
In dev.off() :
unable to open TIFF file 'figures/AES_network_bymembership.tiff'
Kind regards
Sibylle
-Original Message-
From: Ivan Krylov
Sent: Monday, February 26, 2024 10:15 AM
To: SIBYLLE STÖCKLI via R-help
Cc: sibylle.stoec...@gmx.ch
Subject: Re: [R] igraph_vertex
В Mon, 26 Feb 2024 09:02:56 +0100
SIBYLLE STÖCKLI via R-help пишет:
> In the following code, which loads the tiff file, I get the following
> error
This warning is definitely worth investigating, but it shouldn't interrupt your
code. Does the figure come out wrong after you see this warning?
> In doTryCatch(return(expr), name, parentenv, handler) : Character set
> family not found in the Windows character set database
>
> --> I am unsure if mySQL is the right solution. I have no experience
> how to change mySQL.
I see you've tried to do the right thing and searched for the warning message.
Unfortunately, the search engines are wrong; this doesn't seem related to MySQL.
A similarly-worded warning message exists in the Windows-related font functions
inside R:
>> warning(_("font family not found in Windows font database"))
If running a sufficiently new version of R, try Sys.setLanguage('en') before
reproducing the problem and searching for the exact warning message in double
quotes. (Reset it back using
Sys.setLanguage(your_language_code) or restart R afterwards.) Translated error
and warning messages are good for understanding, but they fragment the search
engine results.
I see that a few messages back you set a font family:
> vertex.label.family="Helvetica",
R probably doesn't know where to get it in order to render the plot as TIFF. If
you have a copy of Helvetica installed in your system, try registering it using
windowsFonts(Helvetica = windowsFont("how the font is named in the system")).
(See help(windowsFonts) for more
information.) Otherwise you may be limited to R's predefined font families.
It's annoying that "Helvetica" exists for PDF plots and such seemingly without
a problem, but if you change the output format to TIFF, the set of fonts
available to you changes too. Unfortunately, there are multiple different font
rendering engines in play, and their predefined lists of fonts also differ.
--
Best regards,
Ivan
__
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
В Mon, 26 Feb 2024 09:02:56 +0100
SIBYLLE STÖCKLI via R-help пишет:
> In the following code, which loads the tiff file, I get the following
> error
This warning is definitely worth investigating, but it shouldn't
interrupt your code. Does the figure come out wrong after you see this
warning?
> In doTryCatch(return(expr), name, parentenv, handler) : Character set
> family not found in the Windows character set database
>
> --> I am unsure if mySQL is the right solution. I have no experience
> how to change mySQL.
I see you've tried to do the right thing and searched for the warning
message. Unfortunately, the search engines are wrong; this doesn't seem
related to MySQL.
A similarly-worded warning message exists in the Windows-related font
functions inside R:
>> warning(_("font family not found in Windows font database"))
If running a sufficiently new version of R, try Sys.setLanguage('en')
before reproducing the problem and searching for the exact warning
message in double quotes. (Reset it back using
Sys.setLanguage(your_language_code) or restart R afterwards.)
Translated error and warning messages are good for understanding, but
they fragment the search engine results.
I see that a few messages back you set a font family:
> vertex.label.family="Helvetica",
R probably doesn't know where to get it in order to render the plot as
TIFF. If you have a copy of Helvetica installed in your system, try
registering it using windowsFonts(Helvetica = windowsFont("how the
font is named in the system")). (See help(windowsFonts) for more
information.) Otherwise you may be limited to R's predefined font
families.
It's annoying that "Helvetica" exists for PDF plots and such seemingly
without a problem, but if you change the output format to TIFF, the set
of fonts available to you changes too. Unfortunately, there are
multiple different font rendering engines in play, and their predefined
lists of fonts also differ.
--
Best regards,
Ivan
__
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 Kimmo
First of all many thanks for the valuable advice to publish code and csv.
Noted.
Yes, "edge.width= E(.)$weight" makes definitively sense.
In the following code, which loads the tiff file, I get the following error
tiff("figures/AES_network_bymembership.tiff", width=1000, height=700, res=120)
Warning message:
In doTryCatch(return(expr), name, parentenv, handler) : Character set family
not found in the Windows character set database
--> I am unsure if mySQL is the right solution. I have no experience how to
change mySQL.
Kind regards
Sibylle
tiff("figures/AES_network_bymembership.tiff", width=1000, height=700, res=120)
network %>%
ggraph(., layout = "auto")+
geom_edge_arc(curvature=0.3, aes(width=(E(network)$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)$name), size=5, color="white", repel=T)+
scale_color_scico_d(palette = "batlow")+
scale_edge_width(range = c(0.2,4))+
scale_size(range = c(0.5,20)) +
#scale_edge_color_manual(values = c(scico(21, palette="batlow")))+
theme(plot.background = element_rect(fill = "black"),
legend.position = "right",
panel.background = element_rect(fill = "black"))
dev.off()
-Original Message-
From: R-help On Behalf Of Kimmo Elo
Sent: Monday, February 26, 2024 8:10 AM
To: r-help@r-project.org
Subject: Re: [R] igraph_vertex
Hi,
a quick additional note: try
"edge.width= E(.)$weight"
instead of the current "edge.width= network". Seems to work and makes a visible
difference...
HTH,
Kimmo
su, 2024-02-25 kello 19:11 +, Kimmo Elo kirjoitti:
>
> Hi again,
>
> your code is still not reproducible without modifications, but I
> succeed in getting the data straight. All read.csv-command are missing
> 'sep="\t"', it is need to read you tsv-data.
>
> And it could be more reproducible if you used e.g.
>
> --- snip ---
> aes<-read.csv(text="A.A B.B C.C D.D E.E F.F
> A.A 0 0 5 5 5 5 B.B 4 0
> 1 1 1 1 C.C 5 5 0 5 4
> 2 D.D 5 0 5 0 5 3 E.E 5 1
> 5 5 0 4 F.F 1 2 3 4 5
> 5", sep="\t", row.names = 1)
> --- snip ---
>
> This would save us from unnecessary copy-pasting :-)
>
> However, the error is still the same I mentioned in my first reply,
> i.e.:
>
> network %>% plot(
> vertex.color=clrs[V(.)$community],
> vertex.size=V(.)$hub_score*5,
> vertex.frame.color=V(.)$color,
> vertex.label.color="white",
> vertex.label.cex=0.5,
> vertex.label.family="Helvetica",
> vertex.label.font=1,
> edge.curved=0.5,
> HERE -->edge.width= network, <-- HERE
> layout=layout_with_mds(.))
>
> Try to comment out his line and see what happens. What network data
> variable should be mapped to edge width?
>
> Best,
> Kimmo
>
> su, 2024-02-25 kello 09:59 +0100, sibylle.stoec...@gmx.ch kirjoitti:
> > Dear coummunity
> >
> > Thanks a lot to David and Kimmo. Yes I see now that I need to
> > provide the two raw tables. Find here the reproducible example.
> >
> > Kind regards
> > Sibylle
> >
> > # R-labraries
> > library(circlize)
> > library(ggplot2)
> > library(igraph)
> > library(tidyverse)
> > library(RColorBrewer)
> > library(stringi)
> > library(scico)
> > library(plotly)
> > library(ggraph)
> >
> >
> > # Tables
> > aes<-read.csv("Test_adjac.csv", row.names = 1)
> > details<-read.csv("Test_cat.csv")
> >
> > # Edge table, reorganisation
> > aes_collapsed<-aes %>%
> > rownames_to_column(var='Names') %>%
> > tidyr::gather(target, weight, 1:ncol(aes)+1) %>%
> > dplyr::filter(weight != 0) %>%
> > mutate(weight = ifelse(weight == "-1", 0, weight)) # here 0 =
> > negative values
> >
> > write.csv(aes_collapsed, "edges_table_Test.csv", row.names = F)
> > edge_list<-read.csv("edges_table_Test.csv")
> >
> > # Network attributes
> > network <- graph_from_data_frame(aes_collapsed, directed= FALSE,
> > vertices = details)
> >
> >
> > temp<-cluster_optimal(network)
> > temp<-cbind(membership=temp$membership, Names=temp$name)
> > aes_collapsed <- aes
Re: [R] igraph_vertex
Hi,
a quick additional note: try
"edge.width= E(.)$weight"
instead of the current "edge.width= network". Seems to work and makes a
visible difference...
HTH,
Kimmo
su, 2024-02-25 kello 19:11 +, Kimmo Elo kirjoitti:
>
> Hi again,
>
> your code is still not reproducible without modifications, but I
> succeed in getting the data straight. All read.csv-command are
> missing
> 'sep="\t"', it is need to read you tsv-data.
>
> And it could be more reproducible if you used e.g.
>
> --- snip ---
> aes<-read.csv(text=" A.A B.B C.C D.D E.E F.F
> A.A 0 0 5 5 5 5
> B.B 4 0 1 1 1 1
> C.C 5 5 0 5 4 2
> D.D 5 0 5 0 5 3
> E.E 5 1 5 5 0 4
> F.F 1 2 3 4 5 5",
> sep="\t", row.names = 1)
> --- snip ---
>
> This would save us from unnecessary copy-pasting :-)
>
> However, the error is still the same I mentioned in my first reply,
> i.e.:
>
> network %>% plot(
> vertex.color=clrs[V(.)$community],
> vertex.size=V(.)$hub_score*5,
> vertex.frame.color=V(.)$color,
> vertex.label.color="white",
> vertex.label.cex=0.5,
> vertex.label.family="Helvetica",
> vertex.label.font=1,
> edge.curved=0.5,
> HERE --> edge.width= network, <-- HERE
> layout=layout_with_mds(.))
>
> Try to comment out his line and see what happens. What network data
> variable should be mapped to edge width?
>
> Best,
> Kimmo
>
> su, 2024-02-25 kello 09:59 +0100, sibylle.stoec...@gmx.ch kirjoitti:
> > Dear coummunity
> >
> > Thanks a lot to David and Kimmo. Yes I see now that I need to
> > provide
> > the two raw tables. Find here the reproducible example.
> >
> > Kind regards
> > Sibylle
> >
> > # R-labraries
> > library(circlize)
> > library(ggplot2)
> > library(igraph)
> > library(tidyverse)
> > library(RColorBrewer)
> > library(stringi)
> > library(scico)
> > library(plotly)
> > library(ggraph)
> >
> >
> > # Tables
> > aes<-read.csv("Test_adjac.csv", row.names = 1)
> > details<-read.csv("Test_cat.csv")
> >
> > # Edge table, reorganisation
> > aes_collapsed<-aes %>%
> > rownames_to_column(var='Names') %>%
> > tidyr::gather(target, weight, 1:ncol(aes)+1) %>%
> > dplyr::filter(weight != 0) %>%
> > mutate(weight = ifelse(weight == "-1", 0, weight)) # here 0 =
> > negative values
> >
> > write.csv(aes_collapsed, "edges_table_Test.csv", row.names = F)
> > edge_list<-read.csv("edges_table_Test.csv")
> >
> > # Network attributes
> > network <- graph_from_data_frame(aes_collapsed, directed= FALSE,
> > vertices = details)
> >
> >
> > temp<-cluster_optimal(network)
> > temp<-cbind(membership=temp$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(.)$color,
> > vertex.label.color="white",
> > vertex.label.cex=0.5,
> > vertex.label.family="Helvetica",
> > vertex.label.font=1,
> > edge.curved=0.5,
> > edge.width= network,
> > layout=layout_with_mds(.))
> >
> > #error
> > Error in intI(i, n = x@Dim[1], dn[[1]], give.dn = FALSE) :
> > Index größer als maximales 6
> >
> > # Test_adjac.csv
> > A.A B.B C.C D.D E.E F.F
> > A.A 0 0 5 5 5 5
> > B.B 4 0 1 1 1 1
> > C.C 5 5 0 5 4 2
> > D.D 5 0 5 0 5 3
> > E.E 5 1 5 5 0 4
> > F.F 1 2 3 4 5 5
> >
> > # Test_cat.csv
> > Names corresponding-
> > NCP CategorySubcategory_typesources.cytos
> > ou
> > rce Factor
> > A.A 7 hydrologic attribute"A" A 1
> > B.B 6, 11 hydrologic
Re: [R] igraph_vertex
Hi again,
your code is still not reproducible without modifications, but I
succeed in getting the data straight. All read.csv-command are missing
'sep="\t"', it is need to read you tsv-data.
And it could be more reproducible if you used e.g.
--- snip ---
aes<-read.csv(text="A.A B.B C.C D.D E.E F.F
A.A 0 0 5 5 5 5
B.B 4 0 1 1 1 1
C.C 5 5 0 5 4 2
D.D 5 0 5 0 5 3
E.E 5 1 5 5 0 4
F.F 1 2 3 4 5 5",
sep="\t", row.names = 1)
--- snip ---
This would save us from unnecessary copy-pasting :-)
However, the error is still the same I mentioned in my first reply,
i.e.:
network %>% plot(
vertex.color=clrs[V(.)$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,
HERE -->edge.width= network, <-- HERE
layout=layout_with_mds(.))
Try to comment out his line and see what happens. What network data
variable should be mapped to edge width?
Best,
Kimmo
su, 2024-02-25 kello 09:59 +0100, sibylle.stoec...@gmx.ch kirjoitti:
> Dear coummunity
>
> Thanks a lot to David and Kimmo. Yes I see now that I need to provide
> the two raw tables. Find here the reproducible example.
>
> Kind regards
> Sibylle
>
> # R-labraries
> library(circlize)
> library(ggplot2)
> library(igraph)
> library(tidyverse)
> library(RColorBrewer)
> library(stringi)
> library(scico)
> library(plotly)
> library(ggraph)
>
>
> # Tables
> aes<-read.csv("Test_adjac.csv", row.names = 1)
> details<-read.csv("Test_cat.csv")
>
> # Edge table, reorganisation
> aes_collapsed<-aes %>%
> rownames_to_column(var='Names') %>%
> tidyr::gather(target, weight, 1:ncol(aes)+1) %>%
> dplyr::filter(weight != 0) %>%
> mutate(weight = ifelse(weight == "-1", 0, weight)) # here 0 =
> negative values
>
> write.csv(aes_collapsed, "edges_table_Test.csv", row.names = F)
> edge_list<-read.csv("edges_table_Test.csv")
>
> # Network attributes
> 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
> Error in intI(i, n = x@Dim[1], dn[[1]], give.dn = FALSE) :
> Index größer als maximales 6
>
> # Test_adjac.csv
> A.A B.B C.C D.D E.E F.F
> A.A 0 0 5 5 5 5
> B.B 4 0 1 1 1 1
> C.C 5 5 0 5 4 2
> D.D 5 0 5 0 5 3
> E.E 5 1 5 5 0 4
> F.F 1 2 3 4 5 5
>
> # Test_cat.csv
> Names corresponding-
> NCP CategorySubcategory_typesources.cytosou
> rce Factor
> A.A 7 hydrologic attribute"A" A 1
> B.B 6, 11 hydrologic attribute"B" B 1
> C.C 1, 14, 15, 16, 17,
> 18 AES intrinsic "C" C 0
> D.D 1, 14, 15, 16, 17,
> 18 AES intrinsic "D" D 0
> E.E 1, 14, 15, 16, 17,
> 18 AES intrinsic "E" E 0
> F.F 7 AES material"F" F 0
>
>
> # edges_tables_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
Re: [R] igraph_vertex
Dear coummunity
Thanks a lot to David and Kimmo. Yes I see now that I need to provide the two
raw tables. Find here the reproducible example.
Kind regards
Sibylle
# R-labraries
library(circlize)
library(ggplot2)
library(igraph)
library(tidyverse)
library(RColorBrewer)
library(stringi)
library(scico)
library(plotly)
library(ggraph)
# Tables
aes<-read.csv("Test_adjac.csv", row.names = 1)
details<-read.csv("Test_cat.csv")
# Edge table, reorganisation
aes_collapsed<-aes %>%
rownames_to_column(var='Names') %>%
tidyr::gather(target, weight, 1:ncol(aes)+1) %>%
dplyr::filter(weight != 0) %>%
mutate(weight = ifelse(weight == "-1", 0, weight)) # here 0 = negative values
write.csv(aes_collapsed, "edges_table_Test.csv", row.names = F)
edge_list<-read.csv("edges_table_Test.csv")
# Network attributes
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
Error in intI(i, n = x@Dim[1], dn[[1]], give.dn = FALSE) :
Index größer als maximales 6
# Test_adjac.csv
A.A B.B C.C D.D E.E F.F
A.A 0 0 5 5 5 5
B.B 4 0 1 1 1 1
C.C 5 5 0 5 4 2
D.D 5 0 5 0 5 3
E.E 5 1 5 5 0 4
F.F 1 2 3 4 5 5
# Test_cat.csv
Names corresponding-NCP CategorySubcategory_type
sources.cytosource Factor
A.A 7 hydrologic attribute"A" A 1
B.B 6, 11 hydrologic attribute"B" B 1
C.C 1, 14, 15, 16, 17, 18 AES intrinsic "C" C 0
D.D 1, 14, 15, 16, 17, 18 AES intrinsic "D" D 0
E.E 1, 14, 15, 16, 17, 18 AES intrinsic "E" E 0
F.F 7 AES material"F" F 0
# edges_tables_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
__
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
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]]
__
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.
__
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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.
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
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
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(.)$color,
vertex.label.color="white",
vertex.label.cex=0.5,
vertex.label.family="Helvetica",
vertex.label.font=1,
edge.curved=0.5,
edge.width= network,
layout=layout_with_mds(.))
edges_table_Test.csv
Names
target
weight
B.B
A.A
4
C.C
A.A
5
D.D
A.A
5
E.E
A.A
5
F.F
A.A
1
C.C
B.B
5
E.E
B.B
1
F.F
B.B
2
A.A
C.C
5
B.B
C.C
1
D.D
C.C
5
E.E
C.C
5
F.F
C.C
3
A.A
D.D
5
B.B
D.D
1
C.C
D.D
5
E.E
D.D
5
F.F
D.D
4
A.A
E.E
5
B.B
E.E
1
C.C
E.E
4
D.D
E.E
5
F.F
E.E
5
A.A
F.F
5
B.B
F.F
1
C.C
F.F
2
D.D
F.F
3
E.E
F.F
4
F.F
F.F
5
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] igraph_vertex
Dear R-community
It would be nice to get some input how to find a solution for the following
error in igraph and vertex setting.
Thank you very much
Sibylle
> par(bg="black")
> network %>% plot(
+ vertex.color=clrs[V(.)$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
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