eead-csic-compbio / get_homologues

GET_HOMOLOGUES: a versatile software package for pan-genome analysis
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Is there a way to make the pdf outputs from get_homologues into svg files? So, they are easily editable through inkscape or adobe illustrator? #76

Closed TommyH-Tran closed 3 years ago

brunocontrerasmoreira commented 3 years ago

Hi @TommyH-Tran , scripts plot_matrix_heatmap.sh and hcluster_pangenome_matrix.sh can produce SVG, so I guess you are referring to compare_clusters.pl and/or plot_pancore_matrix.pl? These currently produce PNG and PDF outfiles, but I guess I can modify them to produce SVG as well, I'll let you know, Bruno

brunocontrerasmoreira commented 3 years ago

I have now updated compare_clusters.pl , parse_pangenome_matrix.pl and plot_pancore_matrix.pl in GitHub. Please try them out (git pull) and let us know how that goes, Bruno

brunocontrerasmoreira commented 3 years ago

Do you have any feedback on this?

TommyH-Tran commented 3 years ago

I have tried out the compare_clusters.pl and it does make the svg file, however the formatting is a bit messy when opened in illustrator as you can see. Although, this can just be fixed with editing probably.

Pangenome venn pdf venn_t0_Cpro.pdf

Pangenome venn svg SVGTESTvenn_t0-01

Same issue with the parse_pangenome_matrix.pl command.

Pangenome matrix pdf pangenome_matrix_t0__shell.pdf

Pangenome matrix svg pangenome_matrix_t0__shell-01

I have not had time to test plot_pancore_matrix.pl, but I am going to guess it will follow suite.

brunocontrerasmoreira commented 3 years ago

So it seems that Illustrator has trouble with the fonts of SVG plots. Can't you import the PDFs with illustrator? That might be your work around?

vinuesa commented 3 years ago

i use pdf2svg for this task: