SpaMTP IS IN AN UPDATED LOCATION! Please visit here:

https://github.com/GenomicsMachineLearning/SpaMTP

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

SpaMTP is an R based wrapper package for Seurat for the analysis of spatial metabolomic data. This user-freindly package contains various function for the analysis, integration and visalisation of multi-modal 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.

Another development version of the github is below

https://github.com/BCRL-tylu/SpaMTP

Installation

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

if (!require("devtools", quietly = TRUE))
    install.packages("devtools")

devtools::install_github("BiomedicalMachineLearning/SpaMTP")

Installing with conda

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

conda create -n SpaMTP -c conda-forge r-base=4.3.3 r-essentials r-devtools
conda activate SpaMTP

Within the SpaMTP environment open R and install SpaMTP packages

devtools::install_github("BiomedicalMachineLearning/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::r-cairo

This should resolve any issues. Rerun:

BiocManager::install("scater")

Cardinal Failed to 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>
      |         ^~~~~~~~~

If EBImage failed to installed it ist most likely due to an issue with the installation of fftwtools

Try:

conda config --add channels conda-forge
conda config --set channel_priority strict

conda install r-fftwtools

Else try:

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

Try in R:

if (!require("BiocManager", quietly = TRUE)) #Check if BiocManager is installed
    install.packages("BiocManager")

BiocManager::install("fftwtools")

If none of the above methods resolve instiallation issues, install Cardinal directly through conda:

conda install bioconda::bioconductor-cardinal  

rgoslin Failed to install

If rgoslin fails to install please head to their github. Alternative, you can try installing through BiocManager or mamba shown below:

BiocManager::install("rgoslin")

or

mamba install bioconductor-rgoslin

For other issue please flag on github under Issues

SpaMTP Vignette

To come:

## To Come ...