proteolizard-vis
A collection of python classes and widgets to visualize timsTOF raw-data.
Context
Dependencies
proteolizard-vis depends on proteolizard-data, which is
necessary for raw data access, querying, and filtering.
Installation
We recommend to install proteolizard-vis into a separate python virtual environment.
Once activated, you can install the package into it as follows:
git clone https://github.com/theGreatHerrLebert/ionmob.git
cd proteolizard-vis
pip install -e .
Data access and filtering
General concepts
Visual selection of a slice of data
from proteolizarddata.data import PyTimsDataHandleDDA
from proteolizardvis.data import DDADataLoader
data_loader = DDADataLoader()
data_loader.display_widgets()
Visual filtering of data
from proteolizardvis.filter import DDAPrecursorFilter
precursor_filter = DDAPrecursorFilter(data_loader=data_loader)
precursor_filter.display_widgets()
Plotting
Point clouds
from proteolizardvis.point import DDAPrecursorPointCloudVis
precursor_pointcloud_vis = DDAPrecursorPointCloudVis(precursor_filter)
precursor_pointcloud_vis.display_widgets()
Surface Plots
from proteolizardvis.surface import TimsSurfaceVisualizer
surface_vis = TimsSurfaceVisualizer(data_loader=data_loader, data_filter=precursor_filter)
surface_vis.display_widgets()
Applying algorithms to raw data and visualize results
from proteolizardvis.cluster import DBSCANVisualizer
dbscan_vis = DBSCANVisualizer(data=precursor_filter)
dbscan_vis.display_widget()
