SpaMTP

New R-based User-Frendly Spatial Metabolomic, Transcriptomic and Proteomic Data Analysis Tool

The goal of SpaMTP is to integrate tools previously designed for analysing different spatial metabolomic, transcriptomic and proteomic data together into a user-freindly package. This will allow users to seamlessly transition, integrate and co-analyse multimodality datasets in particularly focusing on metabolomic/transcriptomics integration. This package includes various functions to preform pre-processing, spatial visualisation, various down-stream biological centered analyses, data integration and data export of Spatial Metabolomic data. In addition, this package has the ability to use both Cardinal (Spatial Metabolomic based software) and Seurat (Spatial Transcriptomic based software) functions.

Installation

You can install the development version of SpaMTP from GitHub with:

# install.packages("devtools")
devtools::install_github("agc888/SpaMTP")

Below is an example of how to set up SpaMTP using a conda environment

conda create -n SpaMTP -c conda-forge r-base r-essentials r-devtools python==3.9.12
conda activate SpaMTP

Within the SpaMTP environment open R and install these dependency packages

# intall various dependency packages

install.packages("BiocManager")
install.packages("pheatmap")


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
    
BiocManager::install("edgeR")
BiocManager::install("SingleCellExperiment")
BiocManager::install("scater")
BiocManager::install("Cardinal")
BiocManager::install("DropletUtils")


if (!require("remotes", quietly = TRUE))
    install.packages("remotes")
    
remotes::install_github("satijalab/seurat", "seurat5", quiet = TRUE)

# install.packages("devtools")
devtools::install_github("agc888/SpaMTP")

Possible Installiation Errors

Cairo failed to install

checking if R was compiled with the RConn patch... no
checking for cairo.h... no
configure: error: Cannot find cairo.h! Please install cairo (http://www.cairographics.org/) and/or set CAIRO_CFLAGS/LIBS correspondingly.
ERROR: configuration failed for package ‘Cairo’

check these libraries exist:

conda install conda-forge::cairo
conda install conda-forge::xorg-libxt

Then try:

conda install conda-forge::r-cairo

This should resolve any issues. Rerun:

BiocManager::install("scater")

Cardinal Failed ot install

ERROR: dependency ‘EBImage’ is not available for package ‘Cardinal’

BiocManager::install("EBImage")

fftwtools.c:28:9: fatal error: fftw3.h: No such file or directory
   28 | #include<fftw3.h>
      |         ^~~~~~~~~

Try:

conda install bioconda::r-fftwtools
conda install conda-forge::fftw

If install.packages(“fftwtools”) still fails then try this:

conda install bioconda::bioconductor-cardinal  

For other issue please flag on github under Issues

SpaMTP Vignette

To come:

## To Come ...