Chromatogram ms_bokeh

This example shows a chromatogram colored by mass trace. Since all fragment ion spectra coelute this provides strong evidence that the peptide is present.

/home/runner/work/pyopenms_viz/pyopenms_viz/pyopenms_viz/_core.py:587: UserWarning:

Duplicate data detected, data will not be aggregated which may lead to unexpected plots. To enable aggregation set `aggregate_duplicates=True`.

figure(

id = 'p1241', …)

above = [],

align = 'auto',

aspect_ratio = None,

aspect_scale = 1,

attribution = [],

background_fill_alpha = 1.0,

background_fill_color = '#ffffff',

below = [LinearAxis(id='p1253', ...)],

border_fill_alpha = 1.0,

border_fill_color = '#ffffff',

center = [Grid(id='p1257', ...), Grid(id='p1262', ...)],

context_menu = None,

css_classes = [],

css_variables = {},

disabled = False,

elements = [],

extra_x_ranges = {},

extra_x_scales = {},

extra_y_ranges = {},

extra_y_scales = {},

flow_mode = 'block',

frame_align = True,

frame_height = None,

frame_width = None,

height = 500,

height_policy = 'auto',

hidpi = True,

hold_render = False,

js_event_callbacks = {},

js_property_callbacks = {},

left = [LinearAxis(id='p1258', ...)],

lod_factor = 10,

lod_interval = 300,

lod_threshold = 2000,

lod_timeout = 500,

margin = None,

match_aspect = False,

max_height = None,

max_width = None,

min_border = 0,

min_border_bottom = None,

min_border_left = None,

min_border_right = None,

min_border_top = None,

min_height = None,

min_width = None,

name = None,

outline_line_alpha = 1.0,

outline_line_cap = 'butt',

outline_line_color = '#e5e5e5',

outline_line_dash = [],

outline_line_dash_offset = 0,

outline_line_join = 'bevel',

outline_line_width = 1,

output_backend = 'canvas',

renderers = [GlyphRenderer(id='p1285', ...), GlyphRenderer(id='p1297', ...), GlyphRenderer(id='p1309', ...), GlyphRenderer(id='p1321', ...), GlyphRenderer(id='p1333', ...), GlyphRenderer(id='p1345', ...), GlyphRenderer(id='p1357', ...), GlyphRenderer(id='p1374', ...)],

reset_policy = 'standard',

resizable = False,

right = [Legend(id='p1360', ...)],

sizing_mode = None,

styles = {},

stylesheets = [],

subscribed_events = PropertyValueSet(),

syncable = True,

tags = [],

title = Title(id='p1244', ...),

title_location = 'above',

toolbar = Toolbar(id='p1250', ...),

toolbar_inner = False,

toolbar_location = 'above',

toolbar_sticky = True,

visible = True,

width = 500,

width_policy = 'auto',

x_range = DataRange1d(id='p1242', ...),

x_scale = LinearScale(id='p1251', ...),

y_range = Range1d(id='p1369', ...),

y_scale = LinearScale(id='p1252', ...))

import pandas as pd
from pyopenms_viz.util import download_file

pd.options.plotting.backend = "ms_bokeh"

# GitHub raw URL (primary) with Zenodo as backup
url = "https://raw.githubusercontent.com/OpenMS/pyopenms_viz/main/test/test_data/ionMobilityTestChromatogramDf.tsv"
backup_url = "https://zenodo.org/records/17904352/files/ionMobilityTestChromatogramDf.tsv?download=1"
local_path = "ionMobilityTestChromatogramDf.tsv"
download_file(url, local_path, backup_url=backup_url)
df = pd.read_csv(local_path, sep="\t")

df.plot(
    kind="chromatogram",
    x="rt",
    y="int",
    by="Annotation",
    legend_config=dict(bbox_to_anchor=(1, 0.7)),
)