Exporting plot data

This tutorial covers how to export plot data in RAW for using in other programs. This is intended to be distinct from saving data in formats that RAW knows how to read (e.g. .dat, .ift, .hdf5 for profiles, IFTs, and series respectively), as the export formats cannot be read back into RAW. Exporting data in this way is most useful for generating your own figures in other software.

The written version of the tutorial follows.

Exporting plot data as csv

The following plots let you right click on the plot and export the data shown on the plot as a csv file:

  • Guinier fit (not the Guinier axes on the Profiles plot panel)

  • Dimensionless Kratky

  • Comparison (Residuals and Ratios)

  • CRYSOL

  • IFT plot panel

We will demonstrate how to do this using the Guinier fit plot.

  1. Load the glucose_isomerase.dat dataset in the reconstruction_data folder.

  2. Open the Guinier fit window by selecting the profile in the control panel and clicking the “Guinier” button.

    • Tip: For the IFT plot panel, the top and bottom plot (P(r) functions and data/fit in q space) export separately, so if you want both you will need to right click and export from both the top and bottom plot. For the other windows listed above, all data on all plots shown is exported at once.

  3. In the Guinier fit window, right click on the plot and select “Export Data as CSV”.

    export_guinier_png

  4. Give the file an appropriate name and location and save the file.

Note: Comma separated value (.csv) files can be read directly by most spreadsheet programs like Excel. They are text files that can be opened and examined directly in a text editor.

Exporting SVD, EFA, and REGALS plot data

SVD, EFA, and REGALS plot data (including the singular values, autocorrelations, forward and backward EFA plots and EFA and REGALS result plots) can be saved from the various analysis windows.

  1. Load the phehc_sec.hdf5 file in the series_data folder.

  2. Open the SVD window by right clicking on the phehc_sec.hdf5 series item and selecting “SVD”.

  3. Use the “Save Plotted Values” button to save the plotted Singular Values and AutoCorrelation values as a .csv file.

    • Tip: If you want to save more values, increase the end value of the plot indexes.

  4. Use the “Save All” button to save the singular values, autocorrelation values, and the left and right singular vectors as a .csv file.

    export_svd_png

  5. Close the SVD window and open the EFA window. Proceed with the EFA analysis until you reach the final results page.

  6. Use the “Save EFA Data (not profiles)” button to save the EFA results that aren’t the profiles in a .csv file. This includes metadata, the concentration profiles, the chi^2 vs. frame, the forward and backward EFA data, the full singular values and the left and right singular vectors for the number of components selected for EFA.

    export_efa_png

  7. Close the EFA window and open the REGALS window. Proceed with the REGALS analysis until you reach the final results page.

  8. Use the “Save REGALS data (not profiles)” button to save the REGALS results that aren’t the profiles in a .csv file. This includes metadata, the concentration profiles, the smoothed concentration profiles, the chi^2 vs. frame, the component P(r) functions if calculated, the forward and backward EFA data, the full singular values and the left and right singular vectors for the number of components selected for REGALS.

    export_regals_png

Exporting series plot data

Series plot data (including the integrated intensity vs. frame and Rg vs. frame values) can be saved from the Series control panel.

  1. Load the baseline.hdf5 file in the series_data folder.

  2. In the Series control panel, right click on the baseline.hdf5 item and select “Export data”.

  3. Save the .csv file with an appropriate filename and location. This file contains some metadata, and the integrated intensity, mean intensity, if appropriate intensity in a fixed q range or at a fixed q value, subtracted intensity (integrated, mean, q range and q value), Rg, Rg uncertainty, I(0), I(0) uncertainty, MW and MW uncertainty from Vc, MW from Vp, and filename for each frame.

    export_series_png

Saving reconstruction plots

The reconstruction plots (dammif/n residual plots and denss residual, convergence and fsc plots) are automatically saved as <prefix>_dammif_results.pdf or <prefix>_denss_results.pdf. However, the data that makes the plots is not necessarily saved.

For DAMMIF/N results, if you want to recreate the residuals plots you can load the .fir file, which has the fit and experimental data, and open those two curves in the Comparison window to make a residual plot. The residual data can be exported from there. Alternatively, you could calculate the normalized residual directly from the data and fit.

For the DENSS results, the convergence data is saved in the _by_step.fit files, the fsc data is saved in the _fsc.dat file, and the fit data is saved in the _map.fit for each individual model.