I new in python, and I looking for some help. I would like to produce a dotplot in python to compare to different sequences, and plot the data according to a specific threshold.
Can anyone guide me, please?
matplotlib is a python 2D plotting library which produces publication
quality figures in a variety of hardcopy formats and interactive
environments across platforms. matplotlib can be used in python
scripts, the python and ipython shell (ala MATLAB®* or Mathematica®†),
web application servers, and six graphical user interface toolkits.
...so it has been 17 months... but maybe you are or someone stumbling across this thread is still interested in Python dotplotting.
We implemented FlexiDot in Python, which is a relative feature-rich dotplot suite, covering many issues you might encounter, if you like dotplots. We try to document FlexiDot usage really well using many examples to ease entry in the dotplotting world.
SInce you specifically address thresholds: You control FlexiDot matching stringency with the wordsize. In addition (as the image below shows), you can allow ambiguous bases (for DNA) or allow substitutions: