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set label/chr size in layout file；add genelabel rotation parameter (customize x and y for rotation with angle 0) #608

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merged 9 commits into from
Nov 24, 2023
Merged

set label/chr size in layout file；add genelabel rotation parameter (customize x and y for rotation with angle 0) #608

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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
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20 changes: 16 additions & 4 deletions jcvi/graphics/synteny.py
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Original file line number Diff line number Diff line change
Expand Up @@ -79,7 +79,10 @@ def __init__(self, row, delimiter=","):
self.label = args[7].strip()
else:
self.label = None

if len(args) > 8:
self.label_fontsize = float(args[8])
else:
self.label_fontsize = 10

class Layout(AbstractLayout):
def __init__(self, filename, delimiter=",", seed: Optional[int] = None):
Expand Down Expand Up @@ -193,6 +196,7 @@ def __init__(
loc_label=True,
gene_labels: Optional[set] = None,
genelabelsize=0,
genelabelrotation=25,
pad=0.05,
vpad=0.015,
extra_features=None,
Expand Down Expand Up @@ -277,7 +281,7 @@ def __init__(
y + height / 2 + genelabelsize * vpad / 3,
markup(gene_name),
size=genelabelsize,
rotation=25,
rotation=genelabelrotation,
ha="left",
va="center",
color="lightslategray",
Expand Down Expand Up @@ -352,13 +356,13 @@ def __init__(
loc_label = label if loc_label else None
if chr_label:
if loc_label:
ax.text(lx, ly + vpad, chr_label, color=layout.color, **kwargs)
ax.text(lx, ly + vpad, chr_label, size=layout.label_fontsize, color=layout.color, **kwargs)
ax.text(
lx,
ly - vpad,
loc_label,
color="lightslategrey",
size=10,
size=layout.label_fontsize,
**kwargs,
)
else:
Expand Down Expand Up @@ -599,6 +603,13 @@ def main():
+ "However, plot may appear visually crowded. "
+ "Reasonably good values are 2 to 6 [Default: disabled]",
)
p.add_option(
"--genelabelrotation",
default=25,
type="int",
help="Rotate gene labels at this angle (anti-clockwise), useful for debugging. "
+ "[Default: 25]",
)
p.add_option(
"--scalebar",
default=False,
Expand Down Expand Up @@ -647,6 +658,7 @@ def main():
extra_features=opts.extra,
gene_labels=gene_labels,
genelabelsize=opts.genelabelsize,
genelabelrotation=opts.genelabelrotation,
scalebar=opts.scalebar,
shadestyle=opts.shadestyle,
glyphstyle=opts.glyphstyle,
Expand Down