Re: [R] geom_edge & color
Dear community
Find enclosed the full working example.
Many thanks
Sibylle
Test_cat.csv
Names
Subcategory_type
sources.cyto
source
Factor
A.A
material
"A"
A
1
B.B
material
"B"
B
1
C.C
regulation
"C"
C
1
D.D
regulation
"D"
D
1
E.E
habitat
"E"
E
1
F.F
cultural
"F"
F
1
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
Edges_table-Test.csv
Names
target
weight
relationship
B.B
A.A
4
pos
C.C
A.A
5
pos
D.D
A.A
5
neg
E.E
A.A
5
pos
F.F
A.A
1
pos
C.C
B.B
5
pos
E.E
B.B
1
pos
F.F
B.B
2
neg
A.A
C.C
5
pos
B.B
C.C
1
pos
D.D
C.C
5
pos
E.E
C.C
5
pos
F.F
C.C
3
pos
A.A
D.D
5
neg
B.B
D.D
1
pos
C.C
D.D
5
pos
E.E
D.D
5
pos
F.F
D.D
4
pos
A.A
E.E
5
pos
B.B
E.E
1
pos
C.C
E.E
4
pos
D.D
E.E
5
pos
F.F
E.E
5
pos
A.A
F.F
5
pos
B.B
F.F
1
neg
C.C
F.F
2
pos
D.D
F.F
3
pos
E.E
F.F
4
pos
F.F
F.F
5
pos
#upload librairies
library(circlize)
library(ggplot2)
library(igraph)
library(tidyverse)
library(RColorBrewer)
library(stringi)
library(scico)
library(plotly)
library(ggraph)
#upload
aes<-read.csv("Test_adjac.csv", row.names = 1)
details<-read.csv("Test_cat.csv")
# adjacency table
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")
#create network and add some necessary attributes (vertices) for the plot
network <- graph_from_data_frame(aes_collapsed, directed= FALSE,
vertices = details)
### network and vertex with 'subcategory_type'
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$membership) %>%
set_edge_attr(name = "color",
value = c(viridis::viridis(21))
[match(E(.)$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((21)))
[match(V(.)$name, c(factor(V(.)$name)))]) %>%
set_vertex_attr(name= "community", value=cluster_optimal(.)$Subcategory_type)
clrs<-scico(3, palette = "batlow")
windowsFonts(Helvetica = windowsFont("Helvetica"))
par(bg="black")
network %>% plot(
vertex.color=clrs[V(.)$community],
vertex.size=V(.)$hub_score*20,
vertex.frame.color=V(.)$color,
vertex.label.color="white",
vertex.label.cex=0.4,
vertex.label.family="Helvetica",
vertex.label.font=0.75,
edge.curved=0.5,
edge.width= E(.)$weight,
edge.color = ifelse(edge_list$relationship == "pos", "blue", "red"),
layout=layout_with_mds(.))
tiff("figures/Test_network_bysubcatecory.tiff", width=1000, height=900, res=120)
network %>%
ggraph(., layout = "auto")+
geom_edge_arc(curvature=0.3, aes(width=(E(network)$weight/10),
color=c("darkblue", "red")[as.factor(edge_list$relationship)], 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)$name), size=3, color="white", repel=T)+
scale_color_scico_d(palette = "batlow")+
scale_edge_width(range = c(0.2,4))+
scale_size(range = c(0.5,15)) +
theme(plot.background = element_rect(fill = "black"),
legend.position = "right",
panel.background = element_rect(fill = "black"))
dev.off()
-Original Message-
From: R-help On Behalf Of Kimmo Elo
Sent: Thursday, March 21, 2024 10:51 AM
To: r-help@r-project.org
Subject: Re: [R] geom_edge & color
Dear Sibylle,
your example is not working! E.g. no data for "aes_collapsed".
Best,
Kimmo
ke, 2024-03-20 kello 19:28 +0100, SIBYLLE STÖCKLI via R-help kirjoitti:
> Dear community
>
> I am using ggraph to plot a network analysis. See part 2 in the
> working example.
> Besides different colors for different groups of nodes:
> --> geom_node_point(aes(size = V(network)$hub_score*200, color=
> as.factor(V(network)$community)))
> I additionally want to consider different colors for different edge
> gro
Re: [R] geom_edge & color
Hi,
this seems to work (assuming that your problem was the setting of
colours...):
--- snip ---
network %>%
ggraph(., layout = "auto") +
# This produces an error...
# geom_edge_arc(curvature=0.3, aes(width=(E(network)$weight/10),
color=c("darkblue", "red")[as.factor(edge_list$relationship)], alpha=0.5))
+
# ... this works :-)
geom_edge_arc(curvature=0.3, aes(width=E(network)$weight/10,
color=edge_list$relationship), alpha=.5) +
scale_edge_color_manual(values=c("pos"="darkblue", "neg"="red")) +
# This does not work either...
# geom_node_point(aes(size = V(network)$hub_score*200, color=
as.factor(V(network)$community))) +
# ... so try this :)
geom_node_point(aes(size = V(network)$hub_score*200,
color=V(network)$Subcategory_type)) +
geom_node_text(aes(label = V(network)$name), size=3, color="white",
repel=T)+
scale_color_scico_d(palette = "batlow")+
scale_edge_width(range = c(0.2,4))+
scale_size(range = c(0.5,15)) +
theme(plot.background = element_rect(fill = "black"),
legend.position = "right",
panel.background = element_rect(fill = "black"))
--- snip ---
At least in my data created with your code, the object "network" does not
have an attribute "community". I use the existing "Subcategory_type"
instead, because I had no time to debug this problem :-)
I do not know whether this produces what you expect or want to visualise.
HTH,
Kimmo
pe, 2024-03-22 kello 08:59 +0100, sibylle.stoec...@gmx.ch kirjoitti:
> Dear community
>
>
>
> Find enclosed the full working example.
>
>
>
> Many thanks
>
> Sibylle
>
>
>
> Test_cat.csv
>
>
> Names
>
> Subcategory_type
>
> sources.cyto
>
> source
>
> Factor
>
>
> A.A
>
> material
>
> "A"
>
> A
>
> 1
>
>
> B.B
>
> material
>
> "B"
>
> B
>
> 1
>
>
> C.C
>
> regulation
>
> "C"
>
> C
>
> 1
>
>
> D.D
>
> regulation
>
> "D"
>
> D
>
> 1
>
>
> E.E
>
> habitat
>
> "E"
>
> E
>
> 1
>
>
> F.F
>
> cultural
>
> "F"
>
> F
>
> 1
>
>
>
> 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
>
>
>
>
>
> Edges_table-Test.csv
>
>
>
>
> Names
>
> target
>
> weight
>
> relationship
>
>
> B.B
>
> A.A
>
> 4
>
> pos
>
>
> C.C
>
> A.A
>
> 5
>
> pos
>
>
> D.D
>
> A.A
>
> 5
>
> neg
>
>
> E.E
>
> A.A
>
> 5
>
> pos
>
>
> F.F
>
> A.A
>
> 1
>
> pos
>
>
> C.C
>
> B.B
>
> 5
>
> pos
>
>
> E.E
>
> B.B
>
> 1
>
> pos
>
>
> F.F
>
> B.B
>
> 2
>
> neg
>
>
> A.A
>
> C.C
>
> 5
>
> pos
>
>
> B.B
>
> C.C
>
> 1
>
> pos
>
>
> D.D
>
> C.C
>
> 5
>
> pos
>
>
> E.E
>
> C.C
>
> 5
>
> pos
>
>
> F.F
>
> C.C
>
> 3
>
> pos
>
>
> A.A
>
> D.D
>
> 5
>
> neg
>
>
> B.B
>
> D.D
>
> 1
>
> pos
>
>
> C.C
>
> D.D
>
> 5
>
> pos
>
>
> E.E
>
> D.D
>
> 5
>
> pos
>
>
> F.F
>
> D.D
>
> 4
>
> pos
>
>
> A.A
>
> E.E
>
> 5
>
> pos
>
>
> B.B
>
> E.E
>
> 1
>
> pos
>
>
> C.C
>
> E.E
>
> 4
>
> pos
>
>
> D.D
>
> E.E
>
> 5
>
> pos
>
>
> F.F
>
> E.E
>
> 5
>
> pos
>
>
> A.A
>
> F.F
>
> 5
>
> pos
>
>
> B.B
>
> F.F
>
> 1
>
> neg
>
>
> C.C
>
> F.F
>
> 2
>
> pos
>
>
> D.D
>
> F.F
>
> 3
>
> pos
>
>
> E.E
>
> F.F
>
> 4
>
> pos
>
>
> F.F
>
> F.F
>
> 5
>
> pos
>
>
>
>
>
>
>
> #upload librairies
>
> library(circlize)
>
> library(ggplot2)
>
> library(igraph)
>
> library(tidyverse)
>
> library(RColorBrewer)
>
> library(stringi)
>
> library(scico)
>
> library(plotly)
>
> library(ggraph)
>
>
>
> #upload
>
> aes<-read.csv("Test_adjac.csv", row.names = 1)
>
> details<-read.csv("Test_cat.csv")
>
>
>
>
>
> # adjacency table
>
> 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")
>
>
>
>
>
> #create network and add some necessary attributes (vertices) for the plot
>
>
>
> network <- graph_from_data_frame(aes_collapsed, directed= FALSE,
>
> vertices = details)
>
>
>
> ### network and vertex with 'subcategory_type'
>
>
>
> 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,
>
>
[R] Double buffering plots on Windows
Hello:
I want to present a sequence of plots as an animation. As a toy example
consider the code
function(n){for (i in 1:n){
plot(1:100,sin(i*(1:100)),type="l")
title(paste("n=",i))
segments(0,0,100,0,col=2)
}}
This sort-of works on a MacOS platform, but the rendering of the plots is a bit
choppy. Inserting a sleep function allows the plots to evolve smoothly.
function(n){for (i in 1:n){
plot(1:100,sin(i*(1:100)),type="l")
title(paste("n=",i))
segments(0,0,100,0,col=2)
Sys.sleep(.2)
}}
However, on a Windows platform, only the last plot is rendered without the
Sys.sleep, so the dynamic element is lost. Inserting the Sys.sleep does allow
all the plots to be rendered, but they seem to be erased before they are drawn
again, so there is substantial flicker in the appearance.
Is there some kind of double-buffering available within R, so that plots are
rendered only after they are fully drawn, leaving the previous plot visible
until it is replaced? I just used the default graphics driver on Windows — is
there perhaps a different driver that will the graphics smoother?
Mik Bickis
Professor Emeritus
Department of Mathematics and Statistics
University of Saskatchewan
__
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and provide commented, minimal, self-contained, reproducible code.
[R] Error message
Hi all,
I am creating an X1.RData file using the R 4.2.2 library.
x1.R
save(datafilename, file="X1.RData")
When I am trying to load this file using another script
X2.R
load("X1.RData")
I am getting this error message:
Error in load("X1.RData", :
bad restore file magic number (file may be corrupted) .. no data loaded.
I am using the same R library (R 4.2.2)
What would be the cause for this error message and how to fix it?
Thank you,
__
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Re: [R] Error message
В Fri, 22 Mar 2024 14:02:09 -0500
Val пишет:
> X2.R
> load("X1.RData")
>
> I am getting this error message:
> Error in load("X1.RData", :
> bad restore file magic number (file may be corrupted) .. no data
> loaded.
This error happens very early when R tries to load the file, right
at the first few bytes. Is "X1.RData" large? Can you share it, or at
least a hexadecimal dump of the first few hundred bytes?
--
Best regards,
Ivan
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Error message
Yes, X1.RData is large(more than 40M rows) .
How do I get the first few bytes?
On Fri, Mar 22, 2024 at 2:20 PM Ivan Krylov wrote:
>
> В Fri, 22 Mar 2024 14:02:09 -0500
> Val пишет:
>
> > X2.R
> > load("X1.RData")
> >
> > I am getting this error message:
> > Error in load("X1.RData", :
> > bad restore file magic number (file may be corrupted) .. no data
> > loaded.
>
> This error happens very early when R tries to load the file, right
> at the first few bytes. Is "X1.RData" large? Can you share it, or at
> least a hexadecimal dump of the first few hundred bytes?
>
> --
> Best regards,
> Ivan
__
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Error message
В Fri, 22 Mar 2024 14:31:17 -0500
Val пишет:
> How do I get the first few bytes?
What does file.info('X1.RData') say?
Do you get any output if you run print(readBin('X1.RData', raw(), 128))?
If this is happening on a Linux or macOS machine, the operating system
command xxd -l 128 X1.RData will give the same output in a more
readable manner, but the readBin(...) output from R should be fine too.
--
Best regards,
Ivan
__
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Error message
Here is the first few bytes,
xxd -l 128 X1.RData
: 8d5a 35f8 1ac5 cc14 a04e be5c 572f a3ad .Z5..N.\W/..
0010: 6210 7024 9b58 93c7 34d0 acb7 7a82 3f99 b.p$.X..4...z.?.
0020: 66ce 0ebb 2057 ec36 55b4 0ece a036 695a f... W.6U6iZ
0030: 258b 3493 b661 f620 f7fe ada7 158a 15f7 %.4..a.
0040: e016 a548 6fcb 20c8 6fb4 493d adc9 ea4a ...Ho. .o.I=...J
0050: 0a2b b7cf a416 336e 5e4e abc5 9874 7be3 .+3n^N...t{.
0060: 5a5a 3405 fe35 8a3d ad80 0dc0 ca3e ea7a ZZ4..5.=.>.z
0070: e628 b220 ee50 0b9f 3a81 e971 8a19 4f54 .(. .P..:..q..OT
On Fri, Mar 22, 2024 at 2:36 PM Ivan Krylov wrote:
>
> В Fri, 22 Mar 2024 14:31:17 -0500
> Val пишет:
>
> > How do I get the first few bytes?
>
> What does file.info('X1.RData') say?
>
> Do you get any output if you run print(readBin('X1.RData', raw(), 128))?
>
> If this is happening on a Linux or macOS machine, the operating system
> command xxd -l 128 X1.RData will give the same output in a more
> readable manner, but the readBin(...) output from R should be fine too.
>
> --
> Best regards,
> Ivan
__
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Re: [R] Error message
В Fri, 22 Mar 2024 14:52:05 -0500
Val пишет:
> : 8d5a 35f8 1ac5 cc14 a04e be5c 572f a3ad .Z5..N.\W/..
> 0010: 6210 7024 9b58 93c7 34d0 acb7 7a82 3f99 b.p$.X..4...z.?.
Thank you!
This doesn't look like any structured data to me. In particular, it
doesn't look like something written by R: those created by modern
versions of R with default settings typically start with an "RDX2\n"
(52 44 58 32 0a) or at least "X\n" (58 0a). Could be a middle of
compressed stream, as if the file was truncated while it was being
written.
Do you get similar results with saveRDS(datafilename, 'X1.rds') and
data2 <- readRDS('X1.rds')? Does this happen with other R objects that
you try to save or in your other scripts?
--
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.
[R] Problem with new version of R: Mutated vocals
Dear ladies and gentlemen,
I have recently installed the latest version of R (4.3.3) for windows. Now I
have the following problems with mutated vowels like �, �, etc. Here is an
example:
If I type the command:
Dir <- "C/Users/macho/Documents/_LVn/Experimentelle �bungen"
in the R console there is no problem. However, if I put the same command into a
source file (e.g. Test.r) and call this file from R (via the source command), I
get the following error message:
> source("C:\\Users\\macho\\Documents\\_LVn\\Experimentelle
> �bungen\\R-Scripts\\R-Dokumentation\\R_scripts zur R_Dokumentation\\Kapitel 4
> Erstellen eines Balkendiagramms\\Test.R")
Fehler: invalid multibyte character in parser
(C:\Users\macho\Documents\_LVn\Experimentelle
�bungen\R-Scripts\R-Dokumentation\R_scripts zur R_Dokumentation\Kapitel 4
Erstellen eines Balkendiagramms\Test.R:1:54
In addition, text files saved with an older version of R (using the function
write.table) containing mutated vowels are not read-in correctly by the
function read.table.
I would be glad, if someone could help me with this problem.
Kind regards,
Siegfried Macho.
--
PD Dr. Siegfried Macho
Psychological Department
University of Fribourg
Rue de Faucigny 2
CH-1700 Fribourg
Tel.: ++41-26-3007635
-
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Re: [R] Problem with new version of R: Mutated vocals
В Fri, 22 Mar 2024 16:11:14 +
MACHO Siegfried via R-help пишет:
> If I type the command:
> Dir <- "C/Users/macho/Documents/_LVn/Experimentelle _bungen"
> in the R console there is no problem. However, if I put the same
> command into a source file (e.g. Test.r) and call this file from R
> (via the source command), I get the following error message:
>
> > source("C:\\Users\\macho\\Documents\\_LVn\\Experimentelle
> > _bungen\\R-Scripts\\R-Dokumentation\\R_scripts zur
> > R_Dokumentation\\Kapitel 4 Erstellen eines
> > Balkendiagramms\\Test.R")
> Fehler: invalid multibyte character in parser
> (C:\Users\macho\Documents\_LVn\Experimentelle
> _bungen\R-Scripts\R-Dokumentation\R_scripts zur
> R_Dokumentation\Kapitel 4 Erstellen eines Balkendiagramms\Test.R:1:54
A few versions ago, the R developers made the change of the encoding
used by R on Windows. Instead of the ANSI encoding, R now uses UTF-8:
https://blog.r-project.org/2020/05/02/utf-8-support-on-windows/index.html
This makes it possible to represent many more characters than the
256-byte range covered by CP1252, but the byte sequences are now
different. Also, non-ASCII characters will take more than one byte to
store.
Can you save the script using the UTF-8 encoding instead of CP1252?
Alternatively, try source(..., encoding = 'CP1252').
> In addition, text files saved with an older version of R (using the
> function write.table) containing mutated vowels are not read-in
> correctly by the function read.table.
In a similar manner, try read.table(..., fileEncoding = 'CP1252').
Setting encoding = 'latin1' may also work, even if it's technically a
different encoding.
--
Best regards,
Ivan
__
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