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fix plot.py to work with kaleido v1 #418

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Merged
wdecoster merged 1 commit into from
Jul 24, 2025
Merged

fix plot.py to work with kaleido v1 #418

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37 changes: 24 additions & 13 deletions nanoplotter/plot.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,9 +3,15 @@
from io import BytesIO
from urllib.parse import quote as urlquote
import sys
from kaleido.scopes.plotly import PlotlyScope
import logging

# bring in kaleido and ensure Chrome is installed
import kaleido
# this will download a small headless Chrome build the first time you run it
kaleido.get_chrome_sync()
Comment on lines +8 to +11
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@microbemarsh microbemarsh Jul 23, 2025

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@wdecoster This should resolve the chrome issue from what I understand.


from kaleido import write_fig_sync


class Plot(object):
"""A Plot object is defined by a path to the output file and the title of the plot."""
Expand All @@ -27,20 +33,18 @@ def encode(self):
return self.encode1()

def encode1(self):
"""Return the base64 encoding of the figure file and insert in html image tag."""
data_uri = b64encode(open(self.path, "rb").read()).decode("utf-8").replace("\n", "")
return '<img src="data:image/png;base64,{0}">'.format(data_uri)

def encode2(self):
"""Return the base64 encoding of the fig attribute and insert in html image tag."""
buf = BytesIO()
self.fig.savefig(buf, format="png", bbox_inches="tight", dpi=100)
buf.seek(0)
string = b64encode(buf.read())
return '<img src="data:image/png;base64,{0}">'.format(urlquote(string))

def save(self, settings):
if not(self.only_report):
if not self.only_report:
if self.html:
with open(self.path, "w") as html_out:
html_out.write(self.html)
Expand All @@ -52,12 +56,10 @@ def save(self, settings):
p = os.path.splitext(self.path)[0] + ".png"
if os.path.exists(p):
os.remove(p)

logging.warning("No static plots are saved due to some kaleido problem:")
logging.warning(e)

elif self.fig:
# if settings["format"] is a list, save the figure in all formats
if isinstance(settings["format"], list):
for fmt in settings["format"]:
self.fig.savefig(
Expand All @@ -66,7 +68,11 @@ def save(self, settings):
bbox_inches="tight",
)
else:
self.fig.savefig(fname=self.path, format=settings["format"], bbox_inches="tight")
self.fig.savefig(
fname=self.path,
format=settings["format"],
bbox_inches="tight",
)
else:
sys.exit("No method to save plot object: no html or fig defined.")

Expand All @@ -77,9 +83,14 @@ def show(self):
sys.stderr.write(".show not implemented for Plot instance without fig attribute!")

def save_static(self, figformat):
scope = PlotlyScope()
with open(self.path.replace("html", figformat), "wb") as f:
f.write(scope.transform(self.fig, format=figformat))
logging.info(
f"Saved {self.path.replace('.html', '')} as {figformat} (or png for --legacy)"
)
"""
Export a Plotly figure via Kaleido v1’s write_fig_sync.
"""
output_path = self.path.replace(".html", f".{figformat}")
try:
write_fig_sync(self.fig, path=output_path)
logging.info(f"Saved {output_path} as {figformat}")
except Exception as e:
logging.warning("No static plots are saved due to some kaleido problem:")
logging.warning(e)

16 changes: 16 additions & 0 deletions scripts/agm_test.sh
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Original file line number Diff line number Diff line change
@@ -0,0 +1,16 @@
#! /bin/bash

#SBATCH --time=04-00:00:00
#SBATCH --partition=defq
#SBATCH --mail-user=myemail@email.org
#SBATCH --mail-type=BEGIN,END,FAIL
#SBATCH --ntasks-per-node=64
#SBATCH --mem=128GB
#SBATCH --nodes=1
#SBATCH --job-name=nplot
#SBATCH --comment=nplot

source /path/to/nanoplot_env/bin/activate

# test fresh nanoplot with kaleido update
NanoPlot --fastq /path/to/test_file.fastq.gz --verbose --minqual 4 --color red -o scripts/agm_tests
2 changes: 2 additions & 0 deletions scripts/agm_tests/LengthvsQualityScatterPlot_dot.html
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2 changes: 2 additions & 0 deletions scripts/agm_tests/LengthvsQualityScatterPlot_kde.html
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