Module Documentation

STREAM.VisualizeTrajectories


LSID
urn:lsid:broad.mit.edu:cancer.software.genepattern.module.analysis:00401
Author(s)
Huidong Chen, Massachussets General Hospital, wrapped as a module by Ted Liefeld, Mesirov Lab, UCSD School of Medicine.
Contact(s)

Algorithm and scientific questions: <Huidong.Chen  at mgh dot harvard dot edu>

Module wrapping issues:  Ted Liefeld  < jliefeld at cloud dot ucsd dot edu>

Introduction

STREAM (Single-cell Trajectories Reconstruction, Exploration And Mapping) is an interactive pipeline capable of disentangling and visualizing complex branching trajectories from both single-cell transcriptomic and epigenomic data. Within GenePattern STREAM is implemented as a collection of modules that cover the entire STREAM processing pipeline to allow individual steps to be performed interactively for data exploration.

STREAM.VisualizeTrajectories is used to generate the subway and stream plots for a computed graph structure.

Huidong to add detail explaining this part of the STREAM pipeline

 

Algorithm

Huidong to cover details of this portion of the analysis

References

H Chen, L Albergante, JY Hsu, CA Lareau, GL Bosco, J Guan, S Zhou, AN Gorban, DE Bauer, MJ Aryee, DM Langenau, A Zinovyev, JD Buenrostro, GC Yuan, L Pinello Single-cell trajectories reconstruction, exploration and mapping of omics data with STREAM. Nature Communications, volume 10, Article number: 1903 (2019)

Nestorowa, S. et al. A single-cell resolution map of mouse hematopoietic stem and progenitor cell differentiation. Blood 128, e20-31 (2016).

Pinello Lab   STREAM Github Repository

ADD GPNB NOTEBOOK HERE WHEN READY

Input Files

  1. data file *
    A STREAM pkl file containing an annotated AnnData matrix of gene expression data.

Output Files

  1. <output filename>_stream_result.pkl
    Output file in STREAM AnnData extended pickle (.pkl) file format suitable for passing to the next step of the STREAM analysis.
  2. S#<output filename>_stream_plot_<gene_name>.png Plot of gene expression across the named stream for the named gene.
  3. S#<output filename>_subwaymap_plot_<gene_name>.png Subway map plot across the named stream for the named gene.
  4. <output filename>_flat_tree.png Tree plot showing all requested gens across the trajectories.

Example Data

Example data for the STREAM workflow can be downloaded from dropbox: Stream Example Data
Ref: Nestorowa, S. et al. A single-cell resolution map of mouse hematopoietic stem and progenitor cell differentiation. Blood 128, e20-31 (2016).

Example data for this specific module is available at stream_epg_result.pkl.

Requirements

GenePattern 3.9.11 or later (dockerized).

Parameters

General

Name Description
data file* A STREAM pkl file containing an annotated AnnData matrix of gene expression data/td>
output filename* The output filename prefix.
root The starting node.
percentile dist Percentile of cells' distances from branches (between 0 and 100) used for calculating the distances between branches of subway map.
preference The preference of nodes. The branch with speficied nodes are preferred and put on the top part of subway plot. The higher ranks the node have, the closer to the top the branch with that node is. e.g. S3,S4.
color by Specify how to color cells.'label': the cell labels. 'branch': the branch id identifed by STREAM.
subway factor The factor used to adjust the distances between branches of subway map.
factor num win The number of sliding windows.
factor min win The factor used to calculate the sliding window size based on shortest branch.
factor width The ratio between length and width of stream plot.

Cell Plots

Name Description
create cell plots Create the cell plots, True/False
log view If True,the number of cells (the width) is logarithmized when outputing stream plot.
factor zoom in If "log view" parameter is True, the factor used to zoom in the thin branches.

Gene Plots

Name Description
create gene plots Create the gene plots, True/False.
genes Comma delimited list of genes, e.g. Car2,Gata1,Epx.

Plotting

Parameters controlling the output figures.
Name Description
figure height Figure height as used in matplotlib graphs. Default=8.
figure width Figure width as used in matplotlib plots. Default=8
figure legend num columns The number of columns that the legend has.

* - required