trace_pearsons

Reliability status: development

Compare multiple chromatin trace tables by computing pairwise distances between barcode combinations and quantifying similarity via Pearson correlation.

This tool is useful for analyzing the structural similarity between different chromatin trace datasets, helping to identify patterns and relationships in chromatin organization across multiple samples or conditions.

usage: trace_pearsons [-h] (--input INPUT [INPUT ...] | --pipe) [-O OUTPUT]
                      [--vmin VMIN] [--vmax VMAX] [--verbose]

Named Arguments

--input

Paths to trace files to compare.

--pipe

Read input filenames from stdin (pipe).

Default: False

-O, --output

Output folder name for the correlation matrix plot (filename: trace_correlation_matrix.png)

Default: '.'

--vmin

Minimum value for colormap scaling

Default: -10

--vmax

Maximum value for colormap scaling

Default: 10

--verbose

Increase verbosity

Default: False

Examples

$ ls *ecsv | trace_pearsons [options]
$ find . -name "*.ecsv" | trace_pearsons [options]

Output

  • A Pearson correlation matrix plot comparing all input trace tables

  • Terminal output showing the numerical correlation values

trace_correlation_matrix

Notes

  • Input files must be in ECSV format compatible with ChromatinTraceTable

  • The script identifies unique parts of filenames to create readable labels in the plot

  • Correlation is calculated based on the spatial distances between barcode pairs