simple utility for parsing and working with NMR peak tables, including ROC analysis
Project description
nmrtoolbox
Introduction
This is a simple utility that provides modules for working with NMRPipe peak tables and performing a receiver operator characteristic (ROC) analysis to quantify the quality of the "recovered" peaks relative to a control set of "synthetic" peaks. The modules in this package are as follows:
nmrtoolbox.peak
: classes for reading in peak tables (currently supports both synthetically generated and recovered peak tables from NMRPipe)nmrtoolbox.roc
: perform receiver operator characteristic (ROC) analysis of a recovered peak table relative to a synthetic peak tablenmrtoolbox.mask
: define regions of a spectrum that contain signal or are emptynmrtoolbox.util
: various supporting utilities used by other modulesnmrtoolbox.strip_plot
: generate color coded strip plots that correspond to the true positive and false positive peaks classified by an ROC analysis
Applications
Example #1 - Formal Workflow
The tools in this package are utilized by the NUScon software package. You can access NUScon on the NMRbox platform (free for academic, government, and non-profit users). Running nuscon -h
will provide instructions on how to run the NUScon evaluation workflow, which directly utilizes the tools presented here in the nmrtoolbox
package.
Example #2 - Kick the Tires
from nmrtoolbox.roc import roc
from nmrtoolbox.strip_plot import strip_plot
# perform ROC analysis and specify filtering criteria
my_roc = roc(
recPeaks=<file-recovered.tab>,
synPeaks=<file-synthetic.tab>,
cluster_type=1,
chi2prob=.75,
vol_height_mismatch=True,
maxLW_percent_SW=0.25,
)
# show and plot results
my_roc.print_stats()
my_roc.plot_roc()
# generate strip plots
strip_plot(
recSpectrum=<file-recovered-spectrum.ft3>,
sumSpectrum=<file-sum-spectrum.ft3>,
empSpectrum=<file-empirical-spectrum.ft3>,
empPeaks=<file-empirical.tab>,
roc_obj=my_roc,
)
The roc function supports the following filter criteria:
number
height
abs_height
roi_list
index
cluster_type
mask_file
chi2prob
outlier
vol_height_mismatch
maxLW_percent_SW
Note: Filtering by mask
requires the external use of NMRPipe to generate a mask file indicating where the spectrum is empty. This binary data is converted by Connjur Spectrum Translator into a "tabular" format file (i.e. plain text) which is then read in by nmrtoolbox.mask
.
The strip plot function shown above will make pairwise comparisons among the following 3 types of input spectra (all of which are fundamental to the NUScon workflow):
- empSpectrum: empirical spectrum, this reference is typically obtained by FT processing of a uniformly collected experiment
- sumSpectrum: sum spectrum, this control is typically obtained by FT processing the uniformly sampled time domain data of the empirical data augmented with synthetic peaks
- recSpectrum: recovered spectrum, typically obtained by processing a nonuniformly sampled version of the empirical time data augmented with the synthetic time data
In addition, the corresponding peak tables are also accepted as inputs:
- empPeaks: empirical peaks, peak table from the empirical spectrum
- synPeaks: synthetic peaks, peak table of just the synthetic peaks used to build the sum spectrum
- recPeaks: recovered peaks, peak table from the NUS reconstruction of the synthetic and empirical data
Example data from NUScon archive is available on NMRbox at '/NUScon/archive'
Changelog
v11
- major upgrades to strip_plot module
- PeakTable and Spectrum classes use enumerated types to define valid input formats
- PeakTable and Spectrum classes offer .read() methods to handle multiple input types
- rename roc input parameters to be consistent with PeakTable and Spectrum classes
- universal change to variable naming: "injected" is no longer used. "synthetic" refers to only the synthetic peaks/spectra and "sum" refers to "empirical" + "synthetic" peaks/spectra
v10
- major change: ROC now sorts peaks by absolute value of intensity (previously used intensity from largest positive down to largest negative)
- new module added for generating strip plots
- add more options for peak table filtering
v9
- change in internal data model for storing metadata in Peak, PeakTable, Mask, ROC, and ROI classes
- allow roc class to accept Mask object (not just mask file)
- approximate maximum LW for injected peaks from X1/X3, etc. parameters in the injected peak table
- function to write NMRPipe peak table to file
v8
- change to MIT license
- box_radius for mask filtering is multidimensional
- improved input options for setting carrier frequency
- axis labels used to verify compatibility of Peak, Mask, ROI, and ROC objects
v7
- addition of
roc
module - addition of
mask
module
v6
- rename package as
nmrtoolbox
- use subclasses to handle NMRPipe peak tables coming from genSimTab or from the peak picker
v5
- new Axis class for containing metadata from peak table header
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