SquigglePlot

Background

When working with signal level data, generating a simple visualisation to help understand the structural breakdown of a nanopore read, or to simply creating a nice figure, and easy to use, multiple format, plotting script is needed. SquigglePlot allows for visualising sections of the signal, as well as implements some simple scaling to clean up hi/low noise, save in multiple formats (pdf, png, etc), and set the DPI of the save file for publications or posters.

Getting Started

SquigglePlot acts as a wrapper for matplotlib in python. Extract your signal with SquigglePull or point it at some fast5 files.

Instructions for use

Provide a top folder path -p, a signal file from SquigglePull.py -s, or an individual fast5 file-i, and SquigglePlot will plot the raw signal for you.

Quick start

Individual File full signal

python SquigglePlot.py -i ~/data/test.fast5

Plot first 2000 data points of each read from signal file and save at 300dpi pdf*

python SquigglePlot.py -s signals.tsv.gz --plot_colour teal -n 2000 --dpi 300 --no_show o--save test.pdf --save_path ./test/plots/

Plot all from top folder in green

python SquigglePlot.py -p ~/data/ --plot_colour -g

Plot between 2 values in pink

python SquigglePlot.py -i ~/data/test.fast5 --plot_colour pink -n 400,1600

Full usage

usage: SquigglePlot.py [-h] [-f F5F | -p F5_PATH | -s SIGNAL | -i IND]
                       [--head] [-n NUM] [--scale_hi SCALE_HI]
                       [--scale_low SCALE_LOW] [--plot_colour PLOT_COLOUR]
                       [--save SAVE] [--save_path SAVE_PATH] [--no_show]
                       [--dpi DPI]

script name - script description

optional arguments:
  -h, --help            show this help message and exit
  -f F5F, --f5f F5F     File list of fast5 paths
  -p F5_PATH, --f5_path F5_PATH
                        Fast5 top dir
  -s SIGNAL, --signal SIGNAL
                        Extracted signal file from SquigglePull
  -i IND, --ind IND     Individual fast5 file
  --head                Header present in signal or flat file
  -n NUM, --Num NUM     Section of signal to look at - -n 2000 or -n 100,1500
  --scale_hi SCALE_HI   Upper limit for signal outlier scaling
  --scale_low SCALE_LOW
                        Lower limit for signal outlier scaling
  --plot_colour PLOT_COLOUR
                        Colour of signal plot, takes any pyplot entry:
                        k,r,b,g,red,blue,etc...
  --save SAVE           Save file readname_saveArg.pdf --save saveArg.pdf, use
                        png, etc for other file types
  --save_path SAVE_PATH
                        Save filepath
  --no_show             Do not show plot (used for saving many)
  --dpi DPI             Change DPI for publication figs, eg: --dpi 300