This is needed when the plot has too many points but you would still want the legend and label to be saved as “pdf” to be editable. Works for large heatmaps too.
ax.scatter(..., rasterized=True)
ax.pcolormeash(..., rasterized=True)Tag / Python
python select items from a list using a boolean array
from itertools import compress
arr = np.array([x=='TRUE' for x in xList]) # Turn a string list to boolean
list(compress(yList, arr))Source:
https://www.geeksforgeeks.org/python-itertools-compress/
Pandas merge or sum values in rows with the same index
When the values are numeric and apply operators:
df.groupby(level=0).sum()
df.groupby(df.index).sum()
df[specifiedColumn].groupby(level=0).sum()When the values are numeric and apply functions:
# Common usage, merging values
df[1].groupby(level=0).apply(lambda xList: ';'.join(list([x for x in xList])))Source:
https://pandas.pydata.org/pandas-docs/version/0.22/generated/pandas.core.groupby.GroupBy.apply.html
https://pandas.pydata.org/docs/reference/api/pandas.core.groupby.GroupBy.sum.html
Python Pandas merge multiple row/column values into one row/column
Merge multiple row or column values into one row or column:
df.loc[colSelected,].apply(lambda x: ';'.join(x.astype(str)), axis=0)
df.loc[,rowSelected].apply(lambda x: ';'.join(x.astype(str)), axis=1)Python matplotlib: all about fonts
Fonts output into pdf as text, not shape, to be recognized in Illustrator:
import matplotlib
matplotlib.rcParams['pdf.fonttype'] = 42
matplotlib.rcParams['ps.fonttype'] = 42Change fonts style for all, change the default:
import matplotlib as mpl
matplotlib.rcParams['font.family'] = 'Arial'Change fonts style for labels, tick marks, and titles: (for each plot, not changing the default)
plt.xlabel('XXXX', fontsize=12, fontname='Arial')
plt.ylabel('XXXXX', fontsize=12, fontname='Arial')
plt.xticks(fontname='Arial')
plt.yticks(fontname='Arial')
plt.title('XXXXX', fontsize=14, fontname='Arial')Change legend font style: (for each plot, not changing the default)
plt.legend(prop=matplotlib.font_manager.FontProperties(family='Arial', size=12, weight='bold', style='normal'))Source:
https://jonathansoma.com/lede/data-studio/matplotlib/exporting-from-matplotlib-to-open-in-adobe-illustrator/
https://stackoverflow.com/questions/20753782/default-fonts-in-seaborn-statistical-data-visualization-in-ipython
https://stackoverflow.com/questions/47112522/matplotlib-how-to-set-legends-font-type
https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.legend.html
Python Jupyter notebook share the variable across notebooks
yourVar = 'data or your variable'
%store yourVar
del yourVar # only deletes the variable in this notebook but not in storeIn the second notebook:
%store -r yourVar # if you have a variable with the same name, it will rewrite it.
yourVarTo list and delete the stored variable:
%store #list variable in store
%store -d yourVar #delete the variable in storeSource:
https://stackoverflow.com/questions/35935670/share-variables-between-different-jupyter-notebooks
https://ipython.org/ipython-doc/rel-0.12/config/extensions/storemagic.html
Ignore row with only NaN in plotHeatmap – deepTools
If there are NaN in the output from computeMatrix, the generated heatmap is not sorted and a warning message stating Mean of empty slice will show up.
To overcome this, those null values need to be replaced using 0 in the computeMatrix step by --missingDataAsZero tag.
computeMatrix scale-regions -S xxx.bw -R xxx.bed --missingDataAsZero -m xxx -b xxx -a xxx --numberOfProcessors xx -o xxx.gz
plotHeatmap -m xxx.gz -out xxx.pngSource:
https://groups.google.com/g/deeptools/c/B55e0kT_0Ec?pli=1
https://github.com/deeptools/deepTools/issues/490
Python remove elements from a list
list.remove('element')Source:
https://www.programiz.com/python-programming/methods/list/remove
Python check if a file or directory exists
import os.path
# Check if a file exist, return True/False
os.path.exists("test.txt")
# Check if a directory exist, return True/False, for >= python3.4
import pathlib
pathlib.Path("test").exists()
Source:
https://www.guru99.com/python-check-if-file-exists.html
Python return os.system and subprocess output as a string
When we want to use Unix command in python we can directly use os.system() to realize it. However, if we only want to return the output as a string, for example, return ls file names into a string, we need to use subprocess.check_out instead.
To note that, the output from subprocess.check_out() is a bytes object instead of a string, thus we need to further decode to transform into a string.
fileList = subprocess.check_output('ls someFolder/*', shell=True).decode('utf-8').strip().split('\n')Source:
https://stackoverflow.com/questions/606191/convert-bytes-to-a-string