nanoplotter

This module provides functions for plotting data extracted from Oxford Nanopore sequencing reads and alignments, but some of it’s functions can also be used for other applications.

This module is essentially deprecated, as the code got copied to NanoPlot and NanoComp themselves. There will be no more updates after nanoplotter v1.10.0.

FUNCTIONS

• Check if a specified color is a valid matplotlib color checkvalidColor(color)
• Check if a specified output format is valid checkvalidFormat(format)
• Create a bivariate plot with dots, hexbins and/or kernel density estimates. Also arguments for specifying axis names, color and xlim/ylim. scatter(x, y, names, path, color, format, plots, stat=None, log=False, minvalx=0, minvaly=0)
• Create cumulative yield plot and evaluate read length and quality over time timePlots(df, path, color, format)
• Create length distribution histogram and density curve lengthPlots(array, name, path, n50, color, format, log=False)
• Create flowcell physical layout in numpy array makeLayout()
• Present the activity (number of reads) per channel on the flowcell as a heatmap spatialHeatmap(array, title, path, color, format)

INSTALLATION

pip install nanoplotter

or

conda install -c bioconda nanoplotter

CITATION

If you use this tool, please consider citing our publication.