I would like to use the correlation values from the corMat to weight the connecting lines in the circosplot as I want to visualise correlations from 0.5 to 1 but also show which connections are the strongest in the same plot. How can I do that?
Hi @stepra ,
I implemented this in a devel version which you can install using
BiocManager::install('aljabadi/mixOmics@devel'). You can see an example in mixOmics/circosPlot-examples.R at 5995d79da559b101e0a89e5743134a2ca56e4d9b · aljabadi/mixOmics · GitHub
You can see
?circosPlot for details.
Please let me know if you have any feedback on this feature.
Excellent! Thank you, Al. I will try it out
Quick question: How do I load the updated devel version?
These alternatives do not work:
Error in library(aljabadi/mixOmics@devel) : ‘package’ must be of length 1
Error in library(mixOmics@devel) : ‘package’ must be of length 1
If i load the package using
package ‘mixOmics’ was built under R version 4.0.2Loading required package: MASS
package ‘MASS’ was built under R version 4.0.2Loading required package: lattice
Loading required package: ggplot2
package ‘ggplot2’ was built under R version 4.0.2
Loaded mixOmics 6.12.2
Thank you for using mixOmics!
Bookdown vignette: https://mixomicsteam.github.io/Bookdown
Questions, issues: Follow the prompts at http://mixomics.org/contact-us
Cite us: citation(‘mixOmics’)
Error in circosPlot(MyResult.diablo, cutoff = 0.5, line = T, showIntraLinks = T, : unused argument (linkWidth = c(1, 10))
circosPlot(MyResult.diablo, cutoff=.5, line=T, showIntraLinks = T,size.variables = 1, size.labels = 2, size.legend=1.8, color.cor=c(“green2”,“orange2”), linkWidth = c(1, 10), color.blocks = c(“purple3”, “magenta3”))
What do I need to do?
Hi @stepra ,
You can try:
Restart R then:
And make sure the package version loaded is >= 6.15.30
I think I have two problems:
when trying to remove the old version of mixOmics, it is not found in my library
Removing package from ‘/Users/stepra/Library/R/4.0/library’
(as ‘lib’ is unspecified)
Error in remove.packages : there is no package called ‘mixOmics’
However, when loading, it is still there as version 6.12.2. How can I find out where the library ended up? Under
/Users/stepra/Library/R/I have two directories; 3.5 and 4 and I cannot find it in either and it was supposed to be built
under R version 4.0.2
and more important, the new install fails:
Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.1 (2020-06-06)
Installing github package(s) ‘aljabadi/mixOmics@devel’
Downloading GitHub repo aljabadi/mixOmics@devel
✓ checking for file ‘/private/var/folders/yd/zqbbw1g92fn_9k467f4ygcydsqyxdg/T/RtmprXsTTj/remotes5462f1cf1ae/aljabadi-mixOmics-42056c1/DESCRIPTION’ …
─ preparing ‘mixOmics’: (457ms)
✓ checking DESCRIPTION meta-information …
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ looking to see if a ‘data/datalist’ file should be added
─ building ‘mixOmics_6.15.32.tar.gz’
Warning: invalid uid value replaced by that for user ‘nobody’
Warning: invalid gid value replaced by that for user ‘nobody’
- installing source package ‘mixOmics’ …
** using staged installation
** byte-compile and prepare package for lazy loading
Error: (converted from warning) package ‘MASS’ was built under R version 4.0.2
ERROR: lazy loading failed for package ‘mixOmics’
- removing ‘/Users/stepra/Library/R/4.0/library/mixOmics’
Error: Failed to install ‘mixOmics’ from GitHub:
(converted from warning) installation of package ‘/var/folders/yd/zqbbw1g92fn_9k467f4ygcydsqyxdg/T//RtmprXsTTj/file54656a76919/mixOmics_6.15.32.tar.gz’ had non-zero exit status
I am not sure how to solve this.
All the best,
This is because you are not using the latest version of R.
This might fix your issue:
remove.packages('mixOmics') Sys.setenv("R_REMOTES_NO_ERRORS_FROM_WARNINGS" = "true") BiocManager::install('aljabadi/mixOmics@devel')
Thank you, Al! This works