Plots coloring in BPGA pan genome analysis pipeline
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3.7 years ago

I am using BPGA linux based tool for pan genome analysis. It runs quite fine and give me results. the only issue is coloring of plots. all plots made by the pipeline are of black/grey color. How can I made them interactive ? is there is any issue in library ? someone kindly guide me.

genome next-gen pan-genome • 1.3k views
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Hi hafiz.talhamalik ,

I have the same problem. have you been able to solve it? Thanks,

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Yes. Just before exiting the program, there are files with .plt extension. you can edit those files and add colors..!!

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Thank you very much for your reply. Could you tell me which of all the .plt files to modify and which script to modify? I have tried but have not been successful. Thank you very much in advance

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It generates multiple .plt files. If I remember correctly following were the names. kegg_plt.plt plots_.plt cog.plt core_plot.plt. as far as editing goes. there are multiple line containing text like this.. set terminal ......... enhanced ....... edit that line and write color after enhanced like this set terminal ......... enhanced color ....... then re-run those files using gnuplot

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Hello hafiz.talhamalik,

I'm facing the same problem of having results with only black and white plots. After done running BPGA, I only got 2 .plt files which named plots_default.plt and plots.plt in the Supporting-files folder. I did not get the kegg_plt.plt plots_.plt cog.plt core_plot.plt files like you :(

I'm running in macOS Monterey 12.7 with BPGA-Version-1.3 and wine stable 9.0, all the steps were performed following the BPGA user manual. While prepping the input for clustering, I got the line "mv: cannot stat ?INPUT_all.ffn?: No such file or directory" but my inputs still prepped and ready for analysis.

Can you please help me to can solve the problem with INPUT_all.ffn file and get output figures with color? Thank you!

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some of those files are intermediary files. Don't run the whole pipeline in one go. run one step and see if the file is generated, if the file is there just edit and rerun that file and then move to the next step of the pipeline.

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