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)Author / bioinfocore
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/
Slurm sbatch specify nodes or node list
#SBATCH --nodelist=node[01-09]
#SBATCH --nodelist=node01Pandas 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
Unix generate a random string
head /dev/urandom | tr -dc A-Za-z0-9 | head -c10
# Assigning it to a variable
ranNum=$(head /dev/urandom | tr -dc A-Za-z0-9 | head -c10)Source:
https://unix.stackexchange.com/questions/230673/how-to-generate-a-random-string
Unix rearrange columns
awk 'BEGIN {FS="\t"; OFS="\t"} {print $2, $3, $4, $1}' input.txt > output.txtFS and OFS specify the input/output separator
Liftover bam files
The most straightforward way is using CrossMap.
Taking from hg19 to hg38 as example:
pip install CrossMap
CrossMap.py bam -a hg19ToHg38.over.chain input.bam output
#.bam extension will be added automaticallygenome liftover chain files can be downloaded here: http://hgdownload.cse.ucsc.edu/goldenpath/hg19/liftOver/ (change according to your needs)
It is suggested to always use ‘-a’ option according to the CrossMap website.
Source:
http://crossmap.sourceforge.net/#convert-bam-cram-sam-format-files
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