quasildr 0.1.0

quasilinear representation methods for single-cellomics data

Quasilinear data representations for single-cell omics data analysis

Quasildr is a python library for quasilinear data representation methods. It mainly implements two methods, a quasilinear data representation or visualization method GraphDR and a generalized trajectory extraction and inference method StructDR (StructDR is based on nonparametric ridge estimation). The Quasildr package is developed for single-cell omics data analysis, but you can use it on other data types as well.

Install

Run pip install . in this directory.

Quick Start

For quick start, see tutorials under ./tutorials/ directory.

An example python snippet that running these methods are below

#GraphDR 
import quasildr.graphdr import graphdr
Z = graphdr(X_pca, regularization=500)

#NRE
import quasildr.structdr import Scms
Z = Z / Z[:,0].std()
s = Scms(Z, bw=0.1, min_radius = 10)
T = s.scms(Z)

If you are analyzing single-cell data, you may consider using our graphical interface for single-cell omics data analysis Trenti.

Documentation

See documentation here.

“Quasilinear” approaches: GraphDR - visualization and general-purpose representation

“Quasilinear” approaches: StructDR - flexible structure extraction and inference of confidence sets

Commandline tools

We provide commandline tools for quick access to most commonly used quasildr functions, with typical data preprocessing and post processing options built-in. You can add the -h option to access help information to each tool.

• run_graphdr.py

python run_graphdr.py ./example/Dentate_Gyrus.spliced_data.gz --pca --plot --log --transpose --max_dim 50 --refine_iter 4 --reg 500 --no_rotation --anno_file ./example/Dentate_Gyrus.anno.gz --anno_column ClusterName 

• run_structdr.py

 python run_structdr.py --input ./example/Dentate_Gyrus.spliced_data.gz.dim50_k10_reg500_n4t12_pca_no_rotation_log_scale_transpose.drgraph --anno_file ./example/Dentate_Gyrus.anno.gz --anno_column ClusterName  --output ./example/Dentate_Gyrus.spliced_data.gz.dim50_k10_reg500_n4t12_pca_no_rotation_log_scale_transpose.drgraph

Graphical Interface

For an example, run python ./trenti/app.py -i ./example/Dentate_Gyrus.data_pca.gz -f ./example/Dentate_Gyrus.spliced_data.gz -a ./example/Dentate_Gyrus.anno.gz --samplelimit=5000 --log --mode graphdr

See ./trenti/README.md for a further example.