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add customize x y for genelabelrotation 0; add --outputprefix for customized output #612

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merged 12 commits into from
Nov 30, 2023
Merged

add customize x y for genelabelrotation 0; add --outputprefix for customized output #612

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a280f7f
add ignore zero anchor parameter for skip no matches in batch search
Tong-Chen Sep 27, 2023
9e108bf
Merge branch 'tanghaibao:main' into main
Tong-Chen Oct 8, 2023
1e1fbd2
ignore blank line in bed
Tong-Chen Nov 18, 2023
2d6b41d
Merge branch 'main' of github.com:Tong-Chen/jcvi into main
Tong-Chen Nov 18, 2023
cfae7ac
Merge branch 'tanghaibao:main' into main
Tong-Chen Nov 19, 2023
1782caa
Merge branch 'tanghaibao:main' into main
Tong-Chen Nov 21, 2023
be4ea21
set label/chr size in layout file
Tong-Chen Nov 22, 2023
42f0cde
Merge branch 'main' of github.com:Tong-Chen/jcvi into main
Tong-Chen Nov 22, 2023
eef8646
add genelabel rotation (customize x and y for rotation with angle 0)
Tong-Chen Nov 22, 2023
e8f9f0a
add customize x y for genelabelrotation 0; add --outputprefix for cus…
Tong-Chen Nov 30, 2023
8cb3931
Merge branch 'main' into main
tanghaibao Nov 30, 2023
824a600
Reverting some changes when I messed up the "Resolving Conflicts" step
tanghaibao Nov 30, 2023
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18 changes: 16 additions & 2 deletions jcvi/graphics/synteny.py
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Original file line number Diff line number Diff line change
Expand Up @@ -295,9 +295,15 @@ def __init__(
)
gp.set_transform(tr)
if genelabelsize and (not gene_labels or gene_name in gene_labels):
if genelabelrotation == 0:
text_x = x1 if x1 > x2 else x2
text_y = y
else:
text_x = (x1 + x2) / 2
text_y = y + height / 2 + genelabelsize * vpad / 3
ax.text(
(x1 + x2) / 2,
y + height / 2 + genelabelsize * vpad / 3,
text_x,
text_y,
markup(gene_name),
size=genelabelsize,
rotation=genelabelrotation,
Expand Down Expand Up @@ -661,6 +667,11 @@ def main():
choices=Shade.Styles,
help="Style of syntenic wedges",
)
p.add_option(
"--outputprefix",
default="",
help="Prefix for the output file",
)
opts, args, iopts = p.set_image_options(figsize="8x7")

if len(args) != 3:
Expand Down Expand Up @@ -697,6 +708,9 @@ def main():
root.set_ylim(0, 1)
root.set_axis_off()

outputprefix = opts.outputprefix
if outputprefix:
pf = outputprefix
image_name = pf + "." + iopts.format
savefig(image_name, dpi=iopts.dpi, iopts=iopts)

Expand Down