This package provides guidance for analysis of spatially resolved tissue (Visium ST), focusing on clonal dynamics derived from inferred copy number status.
Our particular goal has been identification of the "lethal clone", defined as the clone which metasises from primary cancer tissue to lymph nodes. However, this package can be used for any analysis of clonal evolution and/or somatic mosaicism in heterogeneous tissue.
If you need any assistance with running this package, please feel free to contact us via GitHub "issue" messaging
This packages contains 4 major functions.
1 Infer Copy Number Variation based on transcriptomics data.
2 Spatial data wrapper.
3 Heatmap Plots.
4 Dendrogram selector.
This package is based on InferCNV & SpatialInferCNV. SPACEmapX is designed as a helper package for these.
JAGS R libraries: graphics, grDevices, RColorBrewer, gplots, futile.logger, stats, utils, methods, ape, Matrix, fastcluster, dplyr, HiddenMarkov, ggplot2, edgeR, coin, caTools, digest, reshape, rjags, fitdistrplus, future, foreach, doParallel, BiocGenerics, SummarizedExperiment, SingleCellExperiment, tidyr, parallel, coda, gridExtra, argparse
https://github.com/yintz/SPACEmapX/wiki/SPACEmapX-tutorial
The package can be installed through GitHub using;
install.packages("remotes")
remotes::install_github("yintz/SPACEmapX")LoadSTinfo(summary csv file)
LoadSTdata(loadedSTinfoData)
ShowTwigSpotsList(TwigID1,TwigID2,TwigID3,...)
ShowTwig(TwigID)
ShowTwigSectionName(TwigID)SpaceMapX is an R package that collects useful tools for Spatially Resolved Transcriptomics data analysis and visualization.
This package is designed to work with Visium Fresh Frozen, FFPE V1,V2 data only.
If you would like a representative ST test dataset, please try these data [from Erickson et al, Nature 2022; https://www.nature.com/articles/s41586-022-05023-2]. MendeleyRepository.
For more ST data, you can also go to 10X website to download assorted ST datasets [https://www.10xgenomics.com/datasets?query=&page=1&configure%5BhitsPerPage%5D=50&configure%5BmaxValuesPerFacet%5D=1000&refinementList%5Bproduct.name%5D%5B0%5D=Spatial%20Gene%20Expression&refinementList%5Bspecies%5D%5B0%5D=Human&refinementList%5Bchemistry.version%5D%5B0%5D=2].
Cancer Research UK (CRUK) #C57899/A25812 "Spatial Prostate Assessment and Circulating Environment – The SPACE Study"