I followed the tutorial for "Multilayer community detection" (.../Documents/GitHub/muxViz/docs/articles/ml_community.html) but got an error when running

# Show the multiplex network
plot_multiplex3D(g.list, layer.layout=lay, layer.colors=layer.colors,
                         layer.shift.x=0.5, layer.space=2,
                         layer.labels="auto", layer.labels.cex=1.5,
                         node.size.values="auto", node.size.scale=0.8,
                         show.aggregate=T)

Here is the error message:
Error in !is.na(layer.labels) && !is.null(layer.labels) :
'length = 3' in coercion to 'logical(1)'

> !is.na(layer.labels)
[1] TRUE TRUE TRUE
> !is.null(layer.labels)
[1] TRUE

The first line returns 3 TRUE while the second only 1, so when using &&, an error is returned. This seems to be an inherent error in the source code. I suspect this issue should be resolved internally. Please let me know if I am wrong.

The function colourInput() used to be in the shinyjs package. It's been deprecated and moved into colourpicker package for well over a year, and recently it was completely removed from shinyjs. Please update the code to use the colourpicker package instead.

I got a bug report on colourpicker because an error came up because of this daattali/colourpicker#26

I can install the package by using teh devtools without problem, however every time when I load the pkg, Rstudio with crash with fatal error

The session info are as follows:
R version 4.2.0 (2022-04-22 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)

Matrix products: default

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8
[2] LC_CTYPE=Chinese (Simplified)_China.utf8
[3] LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_China.utf8

attached base packages:
[1] stats graphics grDevices utils datasets methods
[7] base

loaded via a namespace (and not attached):
[1] compiler_4.2.0 tools_4.2.0

How to make binary file "multiplex-infomap_linux" like "multiplex-infomap_windows.exe", which cause no "Multimap not found. Only multislice community detection will be available" warning in GUI?

“To speed up your interaction with muxViz, the folder standalone contains some self-explanatory example scripts which show how to use the most salient analytical techniques available in the library:
community_detection.R
connected_components.R
example_coverage_optimized.R
example_coverage.R
example_overlapping_generator.R
example_plot_edgecolored_heatmap_6panels.R
example_plot_edgecolored_paths_coupling.R
example_plot_edgecolored_paths.R
example_plot_edgecolored.R
example_transitivity_new.R
layer-layer_corr.R
multi_motifs.R”

Where are they???

Hi
I am getting an error while installing the package.

Installing package into ‘C:/Users/svishwakarma/Documents/R/win-library/3.5’
(as ‘lib’ is unspecified)
Warning in install.packages :
cannot open compressed file 'muxViz-master/DESCRIPTION', probable reason 'No such file or directory'
Error in install.packages : cannot open the connection

Please let me know what to do in this issue.

I am getting this warning.
Warning in install.packages :
cannot open compressed file 'muxViz-master/DESCRIPTION', probable reason 'No such file or directory'
Error in install.packages : cannot open the connection

muxViz/examples-scripts/example_coverage_optimized.R

Line 104:

cov.mul.appr <- GetCoverageEvolutionEdgeColored(T.mux, Layers, Nodes, TAUS, Approximate=T, Approximate.disconnected=DisconnectedNodes)

Error in GetCoverageEvolutionEdgeColored(T.mux, Layers, Nodes, TAUS, Approximate = T, :
could not find function "GetCoverageEvolutionEdgeColored"

Some similar "could not find function" problem happened in example_coverage.R and example_overlapping_generator.R

i can open 127.0.0.1, but can't import files.

Error : package or namespace load failed for ‘OpenStreetMap’:
loadNamespace()里算'rJava'时.onLoad失败了，详细内容：
调用: fun(libname, pkgname)
错误: JAVA_HOME cannot be determined from the Registry
此外: Warning messages:
1: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
不存在叫‘session’这个名字的程辑包

I have successfully installed muxViz and used the example data for analysis and visualisation. But what should I do with the data if I want to analyse it based on my own data? I hope I can get your help on this! Thanks!

This works well if I import the txt file before I load any other data. However, if I load the graphics after I've loaded the edges. layers and nodes, I get the following error message:

Warning: Error in $<-.data.frame: replacement has 0 rows, data has 1255
  91: stop
  90: $<-.data.frame
  76: observeEventHandler [C:\Users\username\Documents\muxviz\muxViz-master/server.R#8434]
   5: runApp

The picture in the paper: Manlio De Domenico, Mason A. Porter, Alex Arenas, Multilayer Analysis and Visualization of Networks, published in Journal of Complex Networks 3, 159-176 (2015) (Open Access)
is very good.
Is it possible to open the code ?
Or already opened but I didn't find it?

Hi,
is this project unmaintained?
The last commit is dated January 2018, and there are some open issues as well.
Best

I have already installed "shiny", as follows:

could you help me ?
thank you?

When I trying to install your muxViz, there is a error:colourInput() has been moved to the 'colourpicker' package.
I asked others he tell me the colourinput() funcition now is in the colourpicker instead of shinyjs.
I want to konw if I want to modify profile, where should I modify.

R Studio send me this message, please, helpme

Loading required package: RSpectra
Error in library(ShinyDash) : there is no package called ‘ShinyDash’
Además: Warning message:
Error in library(ShinyDash) : there is no package called ‘ShinyDash’ > install.packages("shiny")
WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding:

https://cran.rstudio.com/bin/windows/Rtools/
Warning in install.packages :
package ‘shiny’ is in use and will not be installed

muxViz/examples-scripts/example_transitivity_new.R

line 27
binarizeMatrix()
Is it in library("Binarize") or library("BiTrinA") ?

And line 42
n.tri["mux"] <- GetGlobalNumberTriangles(M, Layers,Nodes)

Error in diag(A) : long vectors not supported yet: array.c:2186

How do I draw the edges between layers?I wish I could draw the edges between layers, but I've been looking at a lot of source code and still don't know how to do it. Hope to get help，thank you so much!

Hi everyone! I've been working on this issue for two days but don't know how to fix it.
Here is my "external edge color and size" file (in txt format separated by space), sure for test, this file contains only 1 row besides the header :

The error says:

In English, it reads, "Error in $<-.data.frame: replacement has 0 row, data has 1".

I googled the error message almost everywhere on stackoverflow and many other websites but still don't know how to fix it.

I've also tried my best to retrieve the record but I don't know where the numbers before the information is, i.e., "91: stop","90:$<-.data.frame", etc, because they are not in muxVizGUI.R, not in server.R, not in ui.R, etc, thus, I cannot fix the problem according to the warning message.

At one time I thought it may be the wrong sequence to import the data before rendering the graph, I've tried:

1. Apply layout-> import my external edges files ->Render network;
2. import my external edges files ->Apply layout->Render network;

But neither of them works since the upload procedure is OK, but always fail in "import" procedure, as prompted by the lower right pop-up info messages.

Does anyone know how to fix the problem? I appreciate any of your help and thanks a lot!

I'm running muxViz through the Docker image. I can import my config file but the paths it lists aren't found by muxViz. I've tried placing all files within the same folder and prefacing filenames with "./" to no avail. Presumably this has something to do with the VM sandbox. How do I get the muxViz Docker to discover my local paths?

I tried switching to R directly but there's an rjava issue with OpenStreetMaps that I can't seem to overcome.

Hi, there appear to be no example scripts in this location, only the README: muxViz/examples-scripts. Would be great if these could be added.

Hi Dear Manlio and other experts,
Unfortunately the results of MuxViz are not shown!
It is important especially for Motifs.
I have tried different R and shiny versions on different Windows.
I would be pleased if you could help me.

Can you please point me to the documentation for the programmatic interface?

Hi, I was looking for the calculation of the betweenness centrality for a multilayer network in muxViz, but I did not find it.

To be precise, in https://github.com/manlius/muxViz/blob/master/R/muxLib_annotated.R, I found
#betweenness
#todo

Is there any other place where I could find the betweenness centrality calculation for a multilayer network?
If available somewhere else, what are the reference papers for such a metric?

All the best,

The website link fails to provide the full paper, ideally, this should be included in the repository as a pdf.,

Hello, I'm running muxViz on a Windows 10 64 bit OS, R version 3.4.3, RStudio version 1.1.423

I've managed to install and run analysis on a dataset and muxViz successfully displayed my rendered multilayer network on the RGL window. However, when I try to export the image (as a png file), I get the following error:

Warning in rgl.snapshot(FILE_RGL_SNAPSHOT) :
RGL: Pixmap save: unable to open file 'C:\Users\SANDRA\Documents\R\muxViz-master"C:\Users\SANDRA\Documents\R\muxViz-master\export\muxViz_05-03-2018_162649_05-03-2018_163223.png"' for writing
Warning in rgl.snapshot(FILE_RGL_SNAPSHOT) : 'rgl.snapshot' failed

When the program is actually trying to export the image, I see that the directory address displayed has both back- and forward slashes, however they do not appear in the resulting Warning message. I also get similar error when I'm trying to generate annular visualizations.

Any suggestions will be appreciated.

I have created the files for a directed multilayer network (Extended_edges_list.txt, Info_Layer.txt, nodes_layout.txt, Config_file.txt) and try to load them into muxViz.
I browse the config file, I choose the Config_file.txt and click Import Network.

Samples of files are shown below:

Sample of Extended_edges_list.txt:

0 1 30 1
.
.
121 2 142 2
.
.
6 1 6 2
.
.
4763 7 4763 6

Info_Layer.txt:

layerID 
1 
2 
3 
4 
5 
6 
7 

sample of nodes_layout.txt:

nodeID 
1
2
.
.
4768

Config_file.txt:
<path goes here>/Extended_edges_list.txt;<path goes here>/Info_Layer.txt;<path goes here>/nodes_layout.txt

The files appear in the Configuration file Table under their corresponding categories but I get the following message in the bottom right of the screen.

ERROR: File does not exist <path goes here>/Info_Layer.txt

I am not sure what is going on or how to address this issue and any help would be most welcome!

Hi MuxViz team!

I am trying to install the MuxViz GUI, and I am struggling because 'rgdal' and 'session' packages no longer supported as of 3 months ago. I wanted to alert you to this issue and ask if you had solutions.
I am attempting to run the following code:
https://github.com/manlius/muxViz/blob/master/gui-old/muxVizGUI.R

R version 4.3.1
R Studio Version 2023.09.1+494

Pasted is my error output:

Error in install.packages : Updating loaded packages
Loading required package: session
Warning in install.packages :
package ‘session’ is not available for this version of R

A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
Loading required package: rgdal
Warning in install.packages :
package ‘rgdal’ is not available for this version of R

A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
Error in library(ShinyDash) : there is no package called ‘ShinyDash’
In addition: Warning messages:
1: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘session’
2: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘rgdal’

Restarting R session...

install.packages("shiny")
trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-x86_64/contrib/4.3/shiny_1.7.5.1.tgz'
Content type 'application/x-gzip' length 4354031 bytes (4.2 MB)
==================================================
downloaded 4.2 MB

The downloaded binary packages are in
/var/folders/k1/tmhjps3x3v182t2gz3tm8nmw0000gn/T//Rtmp3GQ9BV/downloaded_packages
Loading required package: lmerTest
Loading required package: lme4
Loading required package: Matrix

Attaching package: ‘lmerTest’

The following object is masked from ‘package:lme4’:

lmer

The following object is masked from ‘package:stats’:

step

Pasted is my output of my session info:

R version 4.3.1 (2023-06-16)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.0

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/Los_Angeles
tzcode source: internal

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] lmerTest_3.1-3 lme4_1.1-34 Matrix_1.6-1

loaded via a namespace (and not attached):
[1] utf8_1.2.4 generics_0.1.3 stringi_1.7.12 lattice_0.21-8 digest_0.6.33 magrittr_2.0.3
[7] grid_4.3.1 pkgload_1.3.2.1 fastmap_1.1.1 processx_3.8.2 sessioninfo_1.2.2 pkgbuild_1.4.2
[13] urlchecker_1.0.1 ps_1.7.5 promises_1.2.1 purrr_1.0.2 fansi_1.0.5 scales_1.2.1
[19] numDeriv_2016.8-1.1 cli_3.6.1 shiny_1.7.5.1 crayon_1.5.2 rlang_1.1.1 ellipsis_0.3.2
[25] munsell_0.5.0 splines_4.3.1 remotes_2.4.2.1 cachem_1.0.8 devtools_2.4.5 tools_4.3.1
[31] memoise_2.0.1 nloptr_2.0.3 minqa_1.2.5 dplyr_1.1.3 colorspace_2.1-0 ggplot2_3.4.4
[37] httpuv_1.6.12 boot_1.3-28.1 vctrs_0.6.4 R6_2.5.1 mime_0.12 lifecycle_1.0.3
[43] stringr_1.5.0 htmlwidgets_1.6.2 fs_1.6.3 usethis_2.2.2 MASS_7.3-60 miniUI_0.1.1.1
[49] pkgconfig_2.0.3 callr_3.7.3 pillar_1.9.0 later_1.3.1 gtable_0.3.4 profvis_0.3.8
[55] glue_1.6.2 Rcpp_1.0.11 tibble_3.2.1 tidyselect_1.2.0 rstudioapi_0.15.0 xtable_1.8-4
[61] htmltools_0.5.6.1 nlme_3.1-162 compiler_4.3.1 prettyunits_1.1.1

Hi,
I'm new in muxviz, and I want to show my node labels in my multilayer network, the problem when I check the case "Show nodes labels:" in the platform, it shows me only node ids.

My data in my Layout file is like that:
LAYOUT.txt

if can anyone help me in that I would be very thankful.