gunshotmatch_reports.peaks

Peak Report Generator.

Classes:

CSVReports(project)	Class for producing CSV peak reports.
PeakMetadataTable(project)	Helper class for peak metadata for insertion into a PDF or CSV report.
PeakSummary(peak_no, name, rt, area, ...)	Summary data for a ConsolidatedPeak.

Functions:

build_peak_report(project[, pdf_filename, ...])

Construct a peak report for the given project and write to the chosen file.

class CSVReports(project)

Bases: object

Class for producing CSV peak reports.

Parameters:

project (Project) – A GunShotMatch project.

New in version 0.4.0.

Methods:

overview_csv()	Produce an overview report of the peaks, giving the name, retention time and peak area of the peaks.
summary_csv()	Produce a summary report of the peaks, giving the individual retention times and hits.

overview_csv()

Produce an overview report of the peaks, giving the name, retention time and peak area of the peaks.

The output columns are as follows:

• Peak No.

• Name – The name of the top hit

• Rt – Mean retention time

• Area – Mean peak area

• Area % – Mean peak area as a percentage of the largest peak

• MF – Mean match factor for the top hit

• Rejected – Whether the peak has been rejected (e.g. with PeakViewer)

• Min Peak Area – The minimum peak area across the repeats.

• Max Peak Area – The maximum peak area across the repeats.

• Peak Area Range – The difference between the minimum and maximum peak areas.

• Area Range Percent -ve – The difference between the minimum and mean peak areas as a percentage of the mean.

• Area Range Percent +ve – The difference between the maximum and mean peak areas as a percentage of the mean.

The peaks are sorted from largest to smallest.

Changed in version 0.8.0: Added Min Peak Area, Max Peak Area, Peak Area Range, and Area Range Percent columns.

Return type:

str

summary_csv()

Produce a summary report of the peaks, giving the individual retention times and hits.

The table for each peak mirrors the table in the PDF peak report (build_peak_report()). The peaks are sorted from largest to smallest.

Return type:

str

class PeakMetadataTable(project)

Bases: object

Helper class for peak metadata for insertion into a PDF or CSV report.

Parameters:

project (Project) – A GunShotMatch project.

New in version 0.3.0.

Attributes:

area_percentages	Peak areas as percentage of largest peak
max_peak_number	The total number of peaks in the project.
num_rows	Maximum number of rows for the metadata table.
project	A GunShotMatch project.

Methods:

get_summary_for_peak(peak, peak_number)	Return a formatted summary of the peak.
get_table_for_peak(peak, peak_number)	Return tabulated data on the peak, with individual peak areas, retention times, and the top 5 hits.

area_percentages

Peak areas as percentage of largest peak

get_summary_for_peak(peak, peak_number)

Return a formatted summary of the peak.

Parameters:

• peak (ConsolidatedPeak)

• peak_number (int) – The peak number, 1-indexed.

Return type:

PeakSummary

get_table_for_peak(peak, peak_number)

Return tabulated data on the peak, with individual peak areas, retention times, and the top 5 hits.

Parameters:

• peak (ConsolidatedPeak)

• peak_number (int) – The peak number, 1-indexed.

Return type:

List[Tuple[str, str, str, str, str, str, str, str, str]]

max_peak_number

The total number of peaks in the project.

num_rows

Maximum number of rows for the metadata table.

project

A GunShotMatch project.

namedtuple PeakSummary(peak_no, name, rt, area, area_percentage, mf, rejected)

Bases: NamedTuple

Summary data for a ConsolidatedPeak.

Formatted for insertion into a PDF or CSV peak report.

New in version 0.3.0.

Fields:

0.  peak_no (str) – Peak number, 1-indexed

1.  name (str) – The name of the top hit

2.  rt (str) – Mean retention time

3.  area (str) – Mean peak area

4.  area_percentage (str) – Mean peak area as a percentage of the largest peak

5.  mf (str) – Mean match factor for the top hit

6.  rejected (str) – Whether the peak has been rejected (e.g. with PeakViewer)

__repr__()

Return a nicely formatted representation string

build_peak_report(project, pdf_filename=None, *, title_every_page=False)

Construct a peak report for the given project and write to the chosen file.

Parameters:

• project (Project)

• pdf_filename (Union[str, Path, PathLike, None]) – Optional output filename. Defaults to project_name_peak_report.pdf.

Return type:

str

Returns:

The output filename.