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Launching KPTracer VISION Reports

Introduction

This vignette serves as a tutorial for downloaiding and launching interactive VISION reports for the KP-Tracer dataset. More specifically, this dataset consists of paired scRNA-seq and inferred single-cell phylogenies for tumors from the KP mouse model of non-small-cell lung cancer (as described in Yang et al, bioRxiv 2021). Below, we demonstrate how to download pre-run reports, as well as launch your own.

Prerequisites

Before getting started, you'll have to make sure you have a working version of VISION installed. You can install VISION directly from Github. You can do this in two ways -- either by first cloning the repository and installing from source, or using devtools as described below.

require(devtools)
install_github("YosefLab/VISION")

Also, if you'd like to run your own PhyloVision analyses using the script in our Github repository, you'll have to make sure you have the following packages installed:

install.packages('reticulate')
install.packages('ape')
install.packages('Matrix')

Downloading existing reports

Downloading an existing report is easy as we've hosted these on Zenodo, and R can download data from an existing URL. You can view the reports available on our VISION reports repository here. There are two types of reports:

  1. Basic scRNA-seq VISION reports providing for the sgNT dataset and full dataset; and
  2. PhyloVision reports for individual clones which allow you to probe the phylogenies and scRNA-seq for a specific tumor.

After you pick a report to view (for example 3513_NT_T2 PhyloVision), you can download the report and view the report as so:

url_location = 'https://zenodo.org/record/5888896/files/3513_NT_T2_phylovision.rds?download=1'
vision_report = readRDS(url(url_location))

viewResults(vision_report, port=8119)

The viewResults function will launch a report locally at port 8119. If you are trying to launch a report from a remote server, try using the following call to viewResults:

viewResults(vision_report, host='0.00.0', port=8119, browser=F)

This will launch a report on your remote server, accessible at https://<servername>:8119/Results.html.

Performing new VISION analyses

If there's a particular clone you'd like to evaluate, you can download raw data from our Zenodo repository (currently under embargoed access) here.

Once you've downloaded this data, you can use the script available on our reproducibility repository for doing this analysis. To use this script, you must provide four arguments:

  • A tumor name that exists in the KPTracer-Data/trees directory
  • The path to the KPTracer-Data directory, downloaded from Zenodo.
  • The path to the directory holding the signatures you'd like to use. The script will use all the signatures stored in this folder, so it is advisable to create a new directory specifically for this analysis. Note: Make sure these are signatures with gene names from mm10! We provide two example signature files for mm10 in our reproducibility repository.
  • The file path at which you'd like to save the analyzed object.

For example, the following can be used to launch the script from command line:

~$ Rscript run_phylovision.R 3513_NT_T2 /path/to/KPTracer-Data/ /path/to/kptracer-signatures/ test_vision.rds

Session Info

sessionInfo()
## R version 3.6.2 (2019-12-12)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 16.04.6 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/atlas-base/atlas/libblas.so.3.0
## LAPACK: /usr/lib/atlas-base/atlas/liblapack.so.3.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## loaded via a namespace (and not attached):
##  [1] BiocManager_1.30.10 compiler_3.6.2      BiocStyle_2.22.0   
##  [4] magrittr_1.5        tools_3.6.2         htmltools_0.4.0    
##  [7] yaml_2.2.1          Rcpp_1.0.5          stringi_1.4.6      
## [10] rmarkdown_2.11      knitr_1.37          stringr_1.4.0      
## [13] xfun_0.29           digest_0.6.20       rlang_0.4.6        
## [16] evaluate_0.14