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mkanai / fujiplot

:mount_fuji: Fuji plot—a circos representation of multiple GWAS results— :mount_fuji:
https://www.nature.com/articles/s41588-018-0047-6
GNU General Public License v3.0
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output_example svg image is empty #9

Closed anbai106 closed 1 year ago

anbai106 commented 1 year ago

Hi,

Thank you for this beautiful visualization! I successfully ran your example after struggling to install Circos on my Mac, but the output images for SVG format are empty.

Do you have a fix for this?

Screenshot 2023-06-25 at 9 05 06 AM

Also, the barplot's color is not correct - black and white...

barplot.pdf

The output log for running the script is here:

  • Fuji plot -- a circos representation of multiple GWAS results

  • Version 1.0.3

  • Masahiro Kanai (mkanai@g.harvard.edu)

  • Harvard Medical School / RIKEN IMS / Osaka Univerisity

  • GNU General Public License v3

    Loading input files...

  • Input data: /Users/username/Project/fujiplot/input_example/input.txt

  • Number of significant SNPs: 1407

  • Number of unique loci: 763

  • Trait list: /Users/username/Project/fujiplot/input_example/traitlist.txt

  • Number of traits: 58 (TC,HDL-C,LDL-C,TG,BS,HbA1c,TP,Alb,NAP,AG,BUN,sCr,eGFR,UA,Na,K,Cl,Ca,P,TBil,ZTT,AST,ALT,ALP,GGT,APTT,PT,Fbg,CK,LDH,CRP,WBC,Neutro,Eosino,Baso,Mono,Lym,RBC,Hb,Ht,MCV,MCH,MCHC,Plt,SBP,DBP,MAP,PP,IVS,PW,LVDd,LVDs,LVM,LVMI,RWT,FS,EF,EA)

  • Number of categories: 9 (Metabolic,Protein,Kidney-related,Electrolyte,Liver-related,Other biochemical,Hematological,Blood pressure,Echocardiographic)

  • Output dir: /Users/username/Project/fujiplot/output_example

Excluded 5 traits because of no significant SNPs (IVS,PW,LVM,LVMI,EA).

Generating configuration and data files for circos...

  • Color configuration: /Users/username/Project/fujiplot/config/color.conf
  • Scatter background configuration: /Users/username/Project/fujiplot/config/scatter_background.conf
  • Highlights data (inter-categorical pleiotropic loci): /Users/username/Project/fujiplot/data_tracks/highlights.txt
  • Scatter plot data (significant loci): /Users/username/Project/fujiplot/data_tracks/scatter.txt
  • Stacked bar plot data (# significant SNPs per locus): /Users/username/Project/fujiplot/data_tracks/stacked.txt
  • Label data (name of inter-categorical pleiotropic loci): /Users/username/Project/fujiplot/data_tracks/label.txt

Calling circos to plot...

  • Call: circos -conf /Users/username/Project/fujiplot/config/circos.conf -debug_group summary

debuggroup summary 0.07s welcome to circos v0.69-6 31 July 2017 on Perl 5.030003 debuggroup summary 0.08s current working directory /Users/username/Project/fujiplot debuggroup summary 0.08s command /Users/username/Software/circos-0.69-6-kanai/bin/circos -conf /Users/username/Project/fujiplot/config/circos.conf -debug_group summary debuggroup summary 0.08s loading configuration from file /Users/username/Project/fujiplot/config/circos.conf debuggroup summary 0.08s found conf file /Users/username/Project/fujiplot/config/circos.conf debuggroup summary 0.13s debug will appear for these features: summary debuggroup summary 0.13s bitmap output image ./output/circos.png debuggroup summary 0.13s SVG output image ./output/circos.svg debuggroup summary 0.13s parsing karyotype and organizing ideograms debuggroup summary 0.16s karyotype has 24 chromosomes of total size 3,095,677,436 debuggroup summary 0.16s applying global and local scaling debuggroup summary 0.16s allocating image, colors and brushes

CIRCOS ERROR 

  cwd: /Users/username/Project/fujiplot

  command: /Users/username/Software/circos-0.69-6-kanai/bin/circos -conf
  /Users/username/Project/fujiplot/config/circos.conf -debug_group summary

There was a problem with True Type font support. Circos could not render text from the font file

  /Users/username/Software/circos-0.69-6-kanai/bin/../fonts/modern/cmuntt.ttf

Please check that gd (system graphics library) and GD (Perl's interface to gd) are compiled with True Type support.

On UNIX systems, try

  gdlib-config --all

and look for GD_FREETYPE in the 'features' line and -lfreetype in the 'libs' line. If these are there, it's likely that your Perl GD module needs recompiling.

For help in installing libgd and/or GD, see

  http://www.perlmonks.org/?node_id=621579

If you are having trouble debugging this error, first read the best practices tutorial for helpful tips that address many common problems

  http://www.circos.ca/documentation/tutorials/reference/best_practices

The debugging facility is helpful to figure out what's happening under the hood

  http://www.circos.ca/documentation/tutorials/configuration/debugging

If you're still stumped, get support in the Circos Google Group.

  http://groups.google.com/group/circos-data-visualization

Please include this error, all your configuration, data files and the version of Circos you're running (circos -v).Do not email me directly -- please use the group.

Stack trace: at /Users/username/Software/circos-0.69-6-kanai/bin/../lib/Circos/Error.pm line 425. Circos::Error::fatal_error("font", "no_ttf", "/Users/username/Software/circos-0.69-6-kanai/bin/../fonts/modern/c"...) called at /Users/username/Software/circos-0.69-6-kanai/bin/../lib/Circos/Font.pm line 192 Circos::Font::get_label_size("font_file", "/Users/username/Software/circos-0.69-6-kanai/bin/../fonts/modern/c"..., "size", 10, "text", "abc123") called at /Users/username/Software/circos-0.69-6-kanai/bin/../lib/Circos/Font.pm line 243 Circos::Font::sanity_check() called at /Users/username/Software/circos-0.69-6-kanai/bin/../lib/Circos.pm line 726 Circos::run("Circos", "debug_group", "summary", "_cwd", "/Users/username/Project/fujiplot", "configfile", "/Users/username/Project/fujiplot/config/circos.conf", "_argv", ...) called at /Users/username/Software/circos-0.69-6-kanai/bin/circos line 536 mv: /Users/username/Project/fujiplot/output/circos.png: No such file or directory

  • Final circos outputs: /Users/username/Project/fujiplot/output_example/circos.{png,svg}.

I know that i can debug into the script fujiplot.R, but if you can quickly spot the issue. It would be greatly appreciated!

Thanks

mkanai commented 1 year ago

Hi, can you take a look at the error messages under *** CIRCOS ERROR ***? Many thanks!

anbai106 commented 1 year ago

Yes, I found that it was because of some incompatibility of some library for Circos -- very annoying to install it to be honest. I will try it on my Linux machine.

Thanks

mkanai commented 1 year ago

I'm going to close this due to inactivity. Please let me know if your issue persists.