Chromatogram retention time visualization

chromatogram-retention-time-visualization

Summary

Generate static or interactive chromatogram plots from mass spectrometry data by mapping retention time (RT) to the x-axis and intensity to the y-axis using pyOpenMS-viz with a specified plotting backend. This skill enables publication-ready visualization of 1D chromatographic traces across multiple plotting backends (matplotlib, bokeh, plotly) while leveraging pandas DataFrames for flexible column mapping.

When to use

Apply this skill when you have mass spectrometry data loaded as a pandas DataFrame with at minimum two numeric columns representing retention time and intensity values, and you need to generate a chromatogram visualization for exploratory analysis, quality control, or publication. Trigger conditions include: (1) data is already in or convertible to a pandas DataFrame from CSV, mzML, or similar MS data formats; (2) you want to inspect peak patterns across the retention time dimension; (3) you need to produce static (matplotlib) or interactive (bokeh/plotly) output suitable for notebooks or web applications.

When NOT to use

• Input data lacks retention time or intensity dimensions — use spectrum or peakmap visualization instead.
• You need 2D or 3D mass spectrometry heatmap output (m/z vs. RT vs. intensity) — use peakmap kind instead.
• Your data is already pre-aggregated into a static image or bitmap — visualization skill is not needed.

Inputs

• pandas DataFrame with numeric 'rt' (retention time) and 'intensity' columns
• mzML file (converted to pandas DataFrame via pyOpenMS or similar loader)
• CSV file with retention time and intensity traces (loaded as pandas DataFrame)

Outputs

• static chromatogram figure (matplotlib.figure.Figure or saved PNG/PDF)
• interactive chromatogram visualization (bokeh Plot or plotly Figure object)
• saved chromatogram file (PNG, PDF, or HTML depending on backend)

How to apply

First, load your mass spectrometry data into a pandas DataFrame, ensuring columns named or mapped to 'rt' (retention time) and 'intensity' exist. Second, select your target plotting backend and configure it via pd.set_option('plotting.backend', 'ms_matplotlib') or the equivalent for bokeh/plotly. Third, call .plot(x='rt', y='intensity', kind='chromatogram') on the DataFrame, optionally using the 'by' parameter to facet by mass-to-charge (m/z) value if multiple traces are present. Fourth, verify the resulting figure displays a line or area plot with retention time on the x-axis and intensity on the y-axis, with peaks corresponding to known compound elution times. Fifth, save the figure as PNG or vector format using matplotlib's savefig() or the backend's equivalent export method. The rationale is that pyOpenMS-viz abstracts backend differences into a unified pandas plotting API, avoiding boilerplate matplotlib/bokeh/plotly code while ensuring column names map correctly to MS semantics.

Related tools

• pyOpenMS-viz (Primary visualization library providing unified pandas plotting API for chromatogram rendering across matplotlib, bokeh, and plotly backends) — https://github.com/OpenMS/pyopenms_viz
• pandas (DataFrame container and manipulation library; .plot() method dispatches to pyOpenMS-viz backend)
• matplotlib (Static chromatogram rendering backend; handles figure generation and file export (PNG, PDF))
• bokeh (Interactive chromatogram rendering backend; enables hover tooltips and browser-based exploration)
• plotly (Interactive chromatogram rendering backend; supports both static and interactive output including 3D variants)

Examples

import pandas as pd; ms_data = pd.read_csv('chromatogram.csv'); pd.set_option('plotting.backend', 'ms_matplotlib'); ms_data.plot(x='rt', y='intensity', kind='chromatogram'); plt.savefig('chromatogram.png', dpi=300)

Evaluation signals

• Output figure displays a line or area plot with retention time values on x-axis and corresponding intensity values on y-axis
• Peak positions in the chromatogram align with expected retention times for known compounds in the sample
• When 'by' parameter is used, faceted subplots correctly separate traces by m/z or other grouping column without data loss
• Figure dimensions, axis labels, and title are readable and conform to publication standards (e.g., high DPI, legible fonts)
• Saved file format (PNG/PDF/HTML) is correct and opens without corruption; file size is appropriate for backend choice

Limitations

• Requires retention time and intensity columns to be present and numeric; missing or null values may cause plot errors or distorted visualization.
• The 'by' parameter assumes a discrete grouping column (e.g., m/z); continuous variables will not facet meaningfully.
• Interactive backends (bokeh, plotly) have limited support for certain advanced matplotlib customizations (e.g., custom colormaps, complex annotations).
• Large datasets (millions of RT-intensity points) may render slowly or consume significant memory in interactive backends; consider downsampling or aggregation.
• Consistent axis scaling and labeling depend on correct column naming; typos or case mismatches will cause KeyError exceptions.

Evidence

• [other] Load mass spectrometry data into pandas DataFrame with retention time (rt) and intensity columns: "Load mass spectrometry data into a pandas DataFrame from a deposited CSV or mzML file containing retention time (rt) and intensity columns."
• [other] Set pandas plotting backend and call .plot() with chromatogram kind parameter: "Set the pandas plotting backend to 'ms_matplotlib' using pd.set_option('plotting.backend', 'ms_matplotlib'). 3. Call the .plot() method on the DataFrame with parameters x='rt', y='intensity',"
• [other] Use 'by' parameter to facet by mass-to-charge when multiple traces present: "Optionally use the 'by' parameter to separate different mass traces if multiple mass-to-charge values are present in the data."
• [other] Save figure using matplotlib savefig for publication and archival: "Save the resulting static figure as a PNG file using matplotlib's savefig() method for publication or archival."
• [readme] pyOpenMS-viz supports multiple plotting backends for static and interactive chromatogram visualization: "Support for multiple plotting backends: matplotlib (static), bokeh and plotly (interactive)"
• [readme] Chromatogram is a supported plot type requiring x and y dimensions: "Chromatogram | x, y | chromatogram | ✓ | ✓ | ✓"
• [intro] pyOpenMS-viz integrates seamlessly with plotting backends and leverages pandas: "integrates seamlessly with various plotting library backends (matpotlib, bokeh and plotly) and leverages the power of Pandas for data manipulation and representation"