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Merged
timosachsenberg merged 4 commits into from
Dec 15, 2025
Merged

Investigate CI failure in pyopenms-docs PR #489

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1c2f6bb
Fix RST indentation bug in interactive_plots.rst for PR #480
claude Dec 15, 2025
36b745e
Remove broken setIntensityRange call in interactive_plots.rst
claude Dec 15, 2025
3f98965
Merge branch 'master' into claude/investigate-ci-failure-JZ0IF
timosachsenberg Dec 15, 2025
94824c8
Use ThresholdMower for intensity filtering in interactive_plots.rst
claude Dec 15, 2025
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27 changes: 15 additions & 12 deletions docs/source/user_guide/interactive_plots.rst
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[blacken-docs] reported by reviewdog 🐶

pyopenms-docs/docs/source/user_guide/interactive_plots.rst

Lines 74 to 84 in 94824c8

raster = (
hd.rasterize(
points,
cmap=process_cmap("blues", provider="bokeh"),
aggregator=ds.sum("inty"),
cnorm="log",
alpha=10,
min_alpha=0,
)
.opts(active_tools=["box_zoom"], tools=["hover"], hooks=[new_bounds_hook])
)

Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,6 @@ interactively zoomed-in if you execute the code in a notebook
import holoviews.operation.datashader as hd
from holoviews.plotting.util import process_cmap
from holoviews import opts, dim
import sys

hv.extension("bokeh")

Expand All @@ -29,13 +28,20 @@ interactively zoomed-in if you execute the code in a notebook
loadopts.setMSLevels([1])
loadopts.setSkipXMLChecks(True)
loadopts.setIntensity32Bit(True)
loadopts.setIntensityRange(oms.DRange1(oms.DPosition1(5000), oms.DPosition1(sys.maxsize)))
loader.setOptions(loadopts)
loader.load("../../../src/data/BSA1.mzML", exp)

# Filter out low-intensity peaks using ThresholdMower
threshold_filter = oms.ThresholdMower()
params = threshold_filter.getDefaults()
params.setValue(b"threshold", 5000.0)
threshold_filter.setParameters(params)
threshold_filter.filterPeakMap(exp)

exp.updateRanges()
expandcols = ["RT", "mz", "inty"]
spectraarrs2d = exp.get2DPeakDataLong(
exp.getMinRT(), exp.getMaxRT(), exp.getMinMZ(), exp.getMaxMZ()
exp.getMinRT(), exp.getMaxRT(), exp.getMinMZ(), exp.getMaxMZ(), 1
)
spectradf = pd.DataFrame(dict(zip(expandcols, spectraarrs2d)))
spectradf = spectradf.set_index(["RT", "mz"])
Expand Down Expand Up @@ -75,17 +81,14 @@ interactively zoomed-in if you execute the code in a notebook
min_alpha=0,
)
.opts(active_tools=["box_zoom"], tools=["hover"], hooks=[new_bounds_hook])
.opts( # weird.. I have no idea why one has to do this. But with one opts you will get an error
plot=dict(
width=800,
height=800,
xlabel="Retention time (s)",
ylabel="mass/charge (Da)",
)
)
)

hd.dynspread(raster, threshold=0.7, how="add", shape="square")
hd.dynspread(raster, threshold=0.7, how="add", shape="square").opts(
width=800,
height=800,
xlabel="Retention time (s)",
ylabel="mass/charge (Da)",
)


Result:
Expand Down