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Lukasz Migas lukasz-migas

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lukasz-migas / amino_acid_plot.py
Created November 1, 2021 16:22
Simple python script to generate an image of amino acid sequence
# make your imports
import matplotlib.pyplot as plt
import matplotlib
import numpy as np
# Based on this image
# https://www.google.com/imgres?imgurl=https%3A%2F%2Fqph.fs.quoracdn.net%2Fmain-qimg-88f77484a87d55f1cd615eb2ca2a8441&imgrefurl=https%3A%2F%2Fwww.quora.com%2FWhat-makes-some-amino-acids-polar-and-nonpolar&tbnid=I9Lczh2TViC1rM&vet=12ahUKEwi1qfv8x_fzAhUIr6QKHfN-A0cQMygDegUIARC4AQ..i&docid=Kf-tNnUawtUyBM&w=624&h=769&q=polar%20and%20non%20polar%20amino%20acids&client=firefox-b-d&ved=2ahUKEwi1qfv8x_fzAhUIr6QKHfN-A0cQMygDegUIARC4AQ
NEGATIVE_AA = "DE"
HYDROPHILIC_AA = "AVILMFYW"
@lukasz-migas
lukasz-migas / jointplot.py
Created September 17, 2019 08:43 — forked from amaloney/jointplot.py
Interactive bokeh plot similar to seaborn's jointplot
import numpy as np
import pandas as pd
import statsmodels.api as sm
from bokeh.application import Application
from bokeh.application.handlers import FunctionHandler
from bokeh.io import output_notebook, show
from bokeh.layouts import gridplot
from bokeh.models import (
ColumnDataSource, CustomJS, HoverTool, LinearAxis, Select
)
@lukasz-migas
lukasz-migas / gist:c744d95ab27bfbc8e2aa9159569945b3
Created March 16, 2018 15:14 — forked from sergey-miryanov/gist:3359203
How to use py2exe with mayavi and enable (from ETS)
import os
import sys
from distutils.core import setup
from distutils.dir_util import copy_tree
from py2exe.build_exe import py2exe
import glob
import zlib
import shutil
@lukasz-migas
lukasz-migas / tSNE with no structure.ipynb
Created February 27, 2018 22:34 — forked from vals/tSNE with no structure.ipynb
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@lukasz-migas
lukasz-migas / temperatureCircle.py
Created December 1, 2017 20:29 — forked from anttilipp/temperatureCircle.py
Code to reproduce the "Temperature Circle" visualization.
#
# Hi all,
# this is the Python code I used to make the visualization "Temperature circle"
# (https://twitter.com/anttilip/status/892318734244884480).
# Please be aware that originally I wrote this for my tests only so the
# code was not ment to be published and is a mess and has no comments.
# Feel free to improve, modify, do whatever you want with it. If you decide
# to use the code, make an improved version of it, or it is useful for you
# in some another way I would be happy to know about it. You can contact me
# for example in Twitter (@anttilip). Unchecked demo data (no quarantees)
@lukasz-migas
lukasz-migas / visualize.py
Created October 21, 2017 21:56 — forked from youralien/visualize.py
some visualization helper functions (specifically useful for understanding feature spaces, and visualizing clustering in KMeans and GMM's) using common plotting libraries like matplotlib and seaborn,
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import matplotlib as mpl
import seaborn as sns
from itertools import combinations, cycle, product
mpl_palette=['r', 'g', 'b', 'c', 'm','y']
cblind_palette=[(230,159,0),(86,180,233),(0,158,115),(240,228,66),(0,114,178),(213,94,0),(204,121,167)]
@lukasz-migas
lukasz-migas / nbstripout
Created July 17, 2017 07:59 — forked from minrk/nbstripout
git pre-commit hook for stripping output from IPython notebooks
#!/usr/bin/env python
"""strip outputs from an IPython Notebook
Opens a notebook, strips its output, and writes the outputless version to the original file.
Useful mainly as a git filter or pre-commit hook for users who don't want to track output in VCS.
This does mostly the same thing as the `Clear All Output` command in the notebook UI.
LICENSE: Public Domain