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