Title Italics

[gbouras13]

Hi @moshi4 ,

Question about italicising the title.

I have code like this in my program pharokka implementing pyCirclize.

    # get only to range of gff - as by default gbk takes all contigs, gff only the first
    gbk = Genbank(gbk_file)

    # instantiate circos
    circos = Circos(sectors={gbk.name: gbk.range_size})

   # example plot name
   plot_title = "Staphylococcus Phage one"

    # title if not blank
    circos.text(plot_title, size=int(title_size), r=190)

By default, the plot_title will always plot the title without italics.

However, for this application, it would be useful if I could italicise certain words (in this case, "Staphylococcus Phage one").

There there an easy way to do this that you know of?

George

[moshi4]

Hi @gbouras13,

pyCirclize is a matplotlib-based library, so you can basically take advantage of matplotlib text styles.
As far as I know, in matplotlib you can set italic text like below.

from pycirclize import Circos
from pycirclize.utils import fetch_genbank_by_accid
from pycirclize.parser import Genbank

# Download `NC_002483` E.coli plasmid genbank
gbk_fetch_data = fetch_genbank_by_accid("NC_002483")
gbk = Genbank(gbk_fetch_data)

# Initialize Circos instance with genome size
circos = Circos(sectors={gbk.name: gbk.range_size})
circos.rect(r_lim=(90, 100), fc="lightgrey", ec="none", alpha=0.5)
sector = circos.sectors[0]

# Plot forward strand CDS
f_cds_track = sector.add_track((95, 100))
f_cds_feats = gbk.extract_features("CDS", target_strand=1)
f_cds_track.genomic_features(f_cds_feats, plotstyle="arrow", fc="salmon", lw=0.5)

# Plot reverse strand CDS
r_cds_track = sector.add_track((90, 95))
r_cds_feats = gbk.extract_features("CDS", target_strand=-1)
r_cds_track.genomic_features(r_cds_feats, plotstyle="arrow", fc="skyblue", lw=0.5)

# Plot title with all italic (use style="italic")
circos.text("Escherichia coli K-12 plasmid F (all italic)", size=14, r=10, deg=0, style="italic")

# Plot title with partial italic (use ${text}$)
circos.text("${Escherichia}$ ${coli}$ K-12 plasmid F (partial italic)", size=14, r=10, deg=180)

circos.savefig("result.png")

result.png

Reference:
https://stackoverflow.com/questions/8376335/styling-part-of-label-in-legend-in-matplotlib

[gbouras13]

This is legendary @moshi4. Works a treat even when I pass the title from a command line argument. Thanks so much once again.

George