Usage¶
Jupyter Notebook interface¶
The first step is to use the buttons to upload the files into the notebook (or generate the template).
Upload datafile. This is always the first thing to do when you first launch the notebook. Use the “Upload datafile” button to select the data file. This will enable the other upload buttons.
Uplaod Database. Use this button to upload the database file into the notebook.
Generate Template Next, if needed, click the “Generate Template” button to create the Template in the folder containing the notebook file. Fill out the file with the experiment’s metadata
Uplaod Template Use this button to upload the template into the notebook.
Now that the different input files are loaded, you can choose if the means should be calculated for the run by clicking or not on the mean export checkbox. Once this is done, fill out the run name (to name the end folder), the dilution factor and the concentration in standard molecule (if calibration is external). Once this is done, press the “Calculate” button to generate the results file. To visualize the data using the plotting module, finish by choosing the plots you want from the multiple selection list, and click the “Make plots” button.
Command Line Interface¶
To process your data, type in a terminal:
nmrquant [command line options]
Here after the available options with their full names are enumerated and detailed.
usage: nmrquant [-h] [-d DATABASE] [-F DILUTION_FACTOR] [-t TEMPLATE]
[-k MAKE_TEMPLATE] [-f FORMAT] [-b {individual,meaned}]
[-l {individual,meaned}] [-m] [-c TSP_CONCENTRATION]
[-e EXPORT] [-v]
datafile
Positional Arguments¶
- datafile
Path to data file to process
Named Arguments¶
- -d, --database
Path to proton database
- -F, --dilution_factor
Dilution factor used to calculate concentrations
Default: 1.11
- -t, --template
Path to template file.
- -k, --make_template
Input path to export template to
- -f, --format
Choose a format for the plots. Choices: svg, png, jpeg
Default: “svg”
- -b, --barplot
Possible choices: individual, meaned
Choose histogram to build. Enter “individual” or “meaned”
- -l, --lineplot
Possible choices: individual, meaned
Choose lineplot to build. Enter “individual” or “meaned”
- -m, --mean
Add if means and stds should be calculated on replicates
Default: False
- -c, --tsp_concentration
Add tsp concentration if calibration is external
- -e, --export
Name for exported file
- -v, --verbose
Add option for debug mode
Default: False
NmrQuant proceeds automatically to the data processing and displays progress and important messages in the standard output.