PeakMap ms_bokeh

This example plots a peakmap with marginals by setting add_marginals=True A chromatogram is shown along the x-axis and a spectrum is shown along the y-axis.

/home/runner/work/pyopenms_viz/pyopenms_viz/pyopenms_viz/_bokeh/core.py:587: UserWarning:


You are attempting to set `plot.legend.orientation` on a plot that has zero legends added, this will have no effect.

Before legend properties can be set, you must add a Legend explicitly, or call a glyph method with a legend parameter set.

GridPlot(

id = 'p1226', …)

align = 'auto',

aspect_ratio = None,

children = [(figure(id='p1115', ...), 0, 1), (figure(id='p1162', ...), 1, 0), (figure(id='p1066', ...), 1, 1)],

cols = None,

context_menu = None,

css_classes = [],

css_variables = {},

disabled = False,

elements = [],

flow_mode = 'block',

height = None,

height_policy = 'auto',

js_event_callbacks = {},

js_property_callbacks = {},

margin = None,

max_height = None,

max_width = None,

min_height = None,

min_width = None,

name = None,

resizable = False,

rows = None,

sizing_mode = None,

spacing = 0,

styles = {},

stylesheets = [],

subscribed_events = PropertyValueSet(),

syncable = True,

tags = [],

toolbar = Toolbar(id='p1225', ...),

toolbar_location = 'above',

visible = True,

width = None,

width_policy = 'auto')

import pandas as pd
from pyopenms_viz.util import download_file

pd.options.plotting.backend = "ms_bokeh"

url = "https://zenodo.org/records/17904352/files/ionMobilityTestFeatureDf.tsv?download=1"
local_path = "ionMobilityTestFeatureDf.tsv"
download_file(url, local_path)
df = pd.read_csv(local_path, sep="\t")

df.plot(
    kind="peakmap",
    x="rt",
    y="mz",
    z="int",
    add_marginals=True,
    aggregate_duplicates=True,
)