mkanai/fujiplot

:mount_fuji: Fuji plot—a circos representation of multiple GWAS results— :mount_fuji:

fujiplot's Issues

Problem with the output figure....

Hi,
I wanted to run now the script with my dataset, and this type of error occurs.....

The output seems empty, are there any limitations with the numbers of traits, since I have 920 traits...

My Trait list looks like this:

[I have in total two categories ..._BASE and .....GROUP]

My input file look like this:

[The trait is basically a mass feature of an unknown compound and the Gene is the same as the Locus ID since I do not have information of the gene in those regions]

EDIT:
Found the problem most likely....

Is there a way to increase the highlighted data points?

EDIT:

Changed it in the housekeeping.config file accordingly [=2.991.000 to be sure], but still indicates that I need to change the threshold from 25.000 up to atleast 29.910.....

Thanks.
Mustafa

Adding more categories/Colors

Hi again,
I wanted to create more then 9 categories, however I was not sure where to get the color codes for more colors then the defined 9 in your example files, to generate more categories.
Thanks in advance.
Mustafa

EDIT:
found out that it is HEX based, should work now I guess.

Error in color

Hi After getting a new set of color according to color hex values, I get the following error:

my categories are having the following hex color. Is there an error with my chosen colors?

Sorry for bothering you, and thank again.
Mustafa
EDIT got it sorry a value was wrong.....

colour gene label by novelty

Hi,

Is there a quick way to change the label color by its novelty (known vs novel)?

Thanks
Rima

Problems with running the script

Hi,
I was trying to reproduce your plots, with your data on Github, however it seems to not work.

I am running your current script on Github in Rstudio with only changing the line 13 into :

CIRCOS_PATH = "C:/Users/bulut/Desktop/Fuji_Plot/circos-0.69-6-kanai/bin/"

[where my circus is located; I am unsing the one that you provide on Github with the patch]

And I get following warning:

The following warning messages in line 42 & 43:

input_fname = normalizePath(args[1])
traitlist_fname = normalizePath(args[2])

Warning message:
In normalizePath(path.expand(path), winslash, mustWork) : path[1]=NA

And therefore in the following steps at line 58 & 59 following error:

df = read.table(input_fname, T, sep = '\t', as.is = T, quote = '', comment.char = '')

traitlist = read.table(traitlist_fname, T, sep = '\t', as.is = T, quote = '', comment.char = '', fileEncoding='utf-8')

Error in file(file, "rt") : invalid 'description' argument

And followed with more errors originating I guess from upstream errors.

More information on circus and perl:

I am running the script on a windows machine.

So far, I installed circos, strawberry perl (incl. All the modules needed for circus via CPAN client).

BUT when I am trying to run circus via perl on CMD it shows an error in not able to find the config file.

I run following line in CMD:

C:\Strawberry\perl\bin>perl C:\Users\bulut\Desktop\Fuji_Plot\circos-0.69-6-kanai\bin\circos

CONFIGURATION FILE ERROR

Circos could not find the configuration file []. To run Circos, you need to

specify this file using the -conf flag. The configuration file contains all

the parameters that define the image, including input files, image size,

formatting, etc.

Thanks a lot,
mustafa

output_example svg image is empty

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?

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 ([email protected])
• 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

Circos vs circlize

Thanks for the awesome package!

As a design question, I wonder why you chose circos and not circlize? Was there additional functionality required in circos?