Spectrum ms_bokeh

This example shows a spectrum. We can add the ion_annotation and sequence annotation by specifying these columns.

Annotation color: None

figure(

id = 'p1597', …)

above = [],

align = 'auto',

aspect_ratio = None,

aspect_scale = 1,

attribution = [],

background_fill_alpha = 1.0,

background_fill_color = '#ffffff',

below = [LinearAxis(id='p1609', ...)],

border_fill_alpha = 1.0,

border_fill_color = '#ffffff',

center = [Grid(id='p1613', ...), Grid(id='p1618', ...), Label(id='p1712', ...), Label(id='p1713', ...), Label(id='p1714', ...), Label(id='p1715', ...), Label(id='p1716', ...), Span(id='p1717', ...)],

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='p1614', ...)],

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='p1641', ...), GlyphRenderer(id='p1653', ...), GlyphRenderer(id='p1665', ...), GlyphRenderer(id='p1677', ...), GlyphRenderer(id='p1689', ...), GlyphRenderer(id='p1701', ...)],

reset_policy = 'standard',

resizable = False,

right = [Legend(id='p1704', ...)],

sizing_mode = None,

styles = {},

stylesheets = [],

subscribed_events = PropertyValueSet(),

syncable = True,

tags = [],

title = Title(id='p1600', ...),

title_location = 'above',

toolbar = Toolbar(id='p1606', ...),

toolbar_inner = False,

toolbar_location = 'above',

toolbar_sticky = True,

visible = True,

width = 500,

width_policy = 'auto',

x_range = Range1d(id='p1718', ...),

x_scale = LinearScale(id='p1607', ...),

y_range = Range1d(id='p1719', ...),

y_scale = LinearScale(id='p1608', ...))

import pandas as pd
from pyopenms_viz.util import download_file

pd.options.plotting.backend = "ms_bokeh"

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

# mirror a reference spectrum with ion and sequence annoations
df.plot(
    x="mz",
    y="intensity",
    kind="spectrum",
    ion_annotation="ion_annotation",
    sequence_annotation="sequence",
)