alphatims.plotting

This module provides basic LC-TIMS-Q-TOF plots.

Functions:

heatmap(df, x_axis_label, y_axis_label[, ...])

Create a scatterplot / heatmap for a dataframe.

line_plot(timstof_data, selected_indices, ...)

Plot an XIC, mobilogram or spectrum as a lineplot.

tic_plot(timstof_data[, title, width, height])

Create a total ion chromatogram (TIC) for the data.
alphatims.plotting.heatmap(df, x_axis_label: str, y_axis_label: str, title: str = '', z_axis_label: str = 'intensity', width: int = 1000, height: int = 320, rescale_to_minutes: bool = True, **kwargs)[source]

Create a scatterplot / heatmap for a dataframe.

The coordinates of the dataframe are projected (i.e. their intensities are summed) on the requested axes.

Parameters

  • df (pd.DataFrame) – A dataframe with coordinates. This should be obtained by slicing an alphatims.bruker.TimsTOF object.

  • x_axis_label (str) –

    A label that is used for projection (i.e. intensities are summed) on the x-axis. Options are:

    • mz

    • rt

    • mobility

  • y_axis_label (str) –

    A label that is used for projection (i.e. intensities are summed) on the y-axis. Options are:

    • mz

    • rt

    • mobility

  • title (str) – The title of this plot. Will be prepended with “Heatmap”. Default is “”.

  • z_axis_label (str) – Should not be set for a 2D scatterplot / heatmap. Default is “intensity”.

  • width (int) – The width of this plot. Default is 1000.

  • height (int) – The height of this plot. Default is 320.

  • rescale_to_minutes (bool) – If True, the rt_values of the dataframe will be divided by 60. WARNING: this updates the dataframe directly and is persistent! Default is True.

  • **kwargs – Additional keyword arguments that will be passed to hv.Scatter.

Returns

A scatter plot projected on the 2 dimensions.

Return type

hv.Scatter

alphatims.plotting.line_plot(timstof_data, selected_indices, x_axis_label: str, title: str = '', y_axis_label: str = 'intensity', remove_zeros: bool = False, trim: bool = True, width: int = 1000, height: int = 320, **kwargs)[source]

Plot an XIC, mobilogram or spectrum as a lineplot.

Parameters

  • timstof_data (alphatims.bruker.TimsTOF) – An alphatims.bruker.TimsTOF data object.

  • selected_indices (np.int64[:]) – The raw indices that are selected for this plot. These are typically obtained by slicing the TimsTOF data object with e.g. data[…, “raw”].

  • x_axis_label (str) –

    A label that is used for projection (i.e. intensities are summed) on the x-axis. Options are:

    • rt

    • mobility

    • mz

  • title (str) – The title of this plot. Will be prepended with “Spectrum”, “Mobilogram” or “XIC”. Default is “”.

  • y_axis_label (str) – Should not be set for a 1D line plot. Default is “intensity”.

  • remove_zeros (bool) – If True, zeros are removed. Note that a line plot connects consecutive points, which can lead to misleading plots if non-zeros are removed. If False, use the full range of the appropriate dimension of the timstof_data. Default is False.

  • trim (bool) – If True, zeros on the left and right are trimmed. Default is True.

  • width (int) – The width of this plot. Default is 1000.

  • height (int) – The height of this plot. Default is 320.

  • **kwargs – Additional keyword arguments that will be passed to hv.Curve.

Returns

A curve plot that represents an XIC, mobilogram or spectrum.

Return type

hv.Curve

alphatims.plotting.tic_plot(timstof_data, title: str = '', width: int = 1000, height: int = 320, **kwargs)[source]

Create a total ion chromatogram (TIC) for the data.

Parameters

  • timstof_data (alphatims.bruker.TimsTOF) – An alphatims.bruker.TimsTOF data object.

  • title (str) – The title of this plot. Will be prepended with “TIC”. Default is False

  • width (int) – The width of this plot. Default is 1000.

  • height (int) – The height of this plot. Default is 320.

  • **kwargs – Additional keyword arguments that will be passed to hv.Curve.

Returns

The TIC of the provided dataset.

Return type

hv.Curve