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.
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.
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