peakplotter 0.5.1

Changelog

• Clicking variants with rsID opens Ensembl page for the clicked variant (if the page exists)
  • Note: The clicking feature isn't available on Jupyter Notebook's html view for unknown reason

peakplotter 0.5.0

Changelog:

• Implemented the --vep-ld command line option

peakplotter 0.4.4

Changelog:

• Added additional attributes to HoverTool (position, allele, p-value)
• Fixed minor issues with processing ensembl_assoc column values
• Added ensembl_consequence_level column.
• Added ensembl_consequence_level filter button in output plot for easier examination high consequence variants

peakplotter 0.4.3

Changelog:

1. Fixed bug where non-tophit variants would get excluded in the .csv and peakplot because LD information was not available for the variant
   • This occurs when there are no individuals with genotypes for both the tophit and other variant
2. Debugged PeakCollection,merge method which were missing some peaks to merge (Issue #16).

peakplotter 0.4.2

Changelog:

1. Debugged PeakCollection.merge where duplicate peaks would appear and cause peakplotter run failure
2. Debugged Ensembl REST API query error when peak region is larger than 5Mb

peakplotter 0.4.1

Changelog:

• --version flag on the command line interface is now functional.
• Fixed problem so that data used to generate .html file now output as .csv file again.

peakplotter 0.4.0

Changelog:

• Big changes in the interactive_manh.py script to generate .html peakplot file.
  • There's now an LD slider at the top of the plot which can be used to hide variants outside the range of the slider.
  • You can now click on the gene view plot's legend to hide and show protein coding and non-protein coding genes.
  • You can now click on the genome view plot's legend to hide and show variants with previous association and variants with no previous association.
  • Genes with no external_name will now display their Ensembl gene ID instead

peakplotter 0.3.1

Changelog since 0.2.2:

• Removed bedtools dependency
• Commented the code responsible for creating red previously associated trait lines in .html peak plots.
• The --flank-bp option now behaves as expected and extends both end of the peak with the top hit as the centre of the plot.
• Replaced print feature with logger functionality and added --debug option.
• Refactoring of code

peakplotter 0.2.2

First development release of peakplotter Python3 package.

Please note that peakplotter is still in active development.

PeakPlotter 2 released

A new, faster and more robust version of PeakPlotter.

• the peak finding code is now in Python, no more missed peaks
• dependencies on legacy perl scripts for querying ensembl have been removed
• existing signals are represented even if the causal variants do not overlap with the study dataset