Weighted correlations in circosplot

Support
1

Hi,
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?
/Stef

2

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.

Cheers

Al

3

Excellent! Thank you, Al. I will try it out :grinning:

4

Quick question: How do I load the updated devel version?
I ran BiocManager::install('aljabadi/mixOmics@devel')

These alternatives do not work:

library(aljabadi/mixOmics@devel)
Error in library(aljabadi/mixOmics@devel) : ‘package’ must be of length 1
library(mixOmics@devel)
Error in library(mixOmics@devel) : ‘package’ must be of length 1

If i load the package using

library(mixOmics)
I get:
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!
Tutorials: http://mixomics.org
Bookdown vignette: https://mixomicsteam.github.io/Bookdown
Questions, issues: Follow the prompts at Contact us | mixOmics
Cite us: citation(‘mixOmics’)

With Error in circosPlot(MyResult.diablo, cutoff = 0.5, line = T, showIntraLinks = T, : unused argument (linkWidth = c(1, 10))
when running
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?
Thank you,
Stef

5

Hi @stepra ,

You can try:

remove.packages('mixOmics')
BiocManager::install('aljabadi/mixOmics@devel')

Restart R then:

library(mixOmics)

And make sure the package version loaded is >= 6.15.30

Cheers

Al

6

Dear Al,
I think I have two problems:

  1. 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

  2. and more important, the new install fails:

    BiocManager::install(‘aljabadi/mixOmics@devel’)
    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
    ** R
    ** data
    ** inst
    ** byte-compile and prepare package for lazy loading
    Error: (converted from warning) package ‘MASS’ was built under R version 4.0.2
    Execution halted
    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,
    Stef
7

Hi @stepra,

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')
8

Thank you, Al! This works :slight_smile: