Issues using plotMatrix

[narzouni]

Hello,
Thank you so much for developing these R interesting packages for Hi-C. I am currently working on MicroC data and I found your book.

I tried to use plotMatrix but it gave an error.

I used a .mcool file (cool).

hic2 <- import(coolf, focus = '1:30000-50000000', resolution = 2000)

Here is the information about hic2:

hic2
HiCExperiment object with 1,326,084 contacts over 24,986 regions

---

fileName: "Lib1_Sample1A_1kb.mcool"
focus: "1:30,000-50,000,000"
resolutions(14): 1000 2000 ... 4096000 8192000
active resolution: 2000
interactions: 730094
scores(2): count balanced
topologicalFeatures: compartments(0) borders(0) loops(0) viewpoints(0)
pairsFile: N/A
metadata(0):

If I try to plot it, it give an error related to the file '/usr/lib/libXrender.1.dylib'. I am using R version 4.4.2 on Mac. Did you ever get this error? Here is the error.

plotMatrix(hic2)
Error: .onLoad failed in loadNamespace() for 'Cairo', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Cairo/libs/Cairo.so':
dlopen(/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Cairo/libs/Cairo.so, 0x0006): Library not loaded: /opt/X11/lib/libXrender.1.dylib
Referenced from: <2B39D2DE-4EEA-3AB3-9BC0-0355BE038E52> /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Cairo/libs/Cairo.so
Reason: tried: '/opt/X11/lib/libXrender.1.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/opt/X11/lib/libXrender.1.dylib' (no such file), '/opt/X11/lib/libXrender.1.dylib' (no such file), '/usr/local/lib/libXrender.1.dylib' (no such file), '/usr/lib/libXrender.1.dylib' (no such file, not in dyld cache)

[js2264]

Hi @narzouni , I don't extensively test packages in mac, but HiContacts should be functional for macs as well, as its tests are successfully executed by the Bioconductor build system. Do you have XQuartz installed? I know on my mac I have it installed, and it is the graphical interface that is opened by Cairo from R, when I plot hic matrices. I would recommand installing XQuartz, then reinstall Cairo R package and HiContacts.