SONAR is the algorithm of cell-type deconvolution for spatial transcriptomics
#library(devtools)
devtools:: install_github("lzygenomics/SONAR")
- R version >= 4.0.5.
- R packages:
- this.path>=0.5.1; Matrix>=1.3.4; data.table>=1.14.0; Seurat>=4.0.3; matlabr=1.5.2; R.matlab=3.7.0
- MATLAB version >= R2019a
- Just install the MATLAB, subsequent operations do not require you to use the MATLAB language
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Install the dependence
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Install SONAR
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Download the SONAR files: Follow the Example/SONAR-entrance.Rmd IS ALL YOU NEED
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/inst/extdata/
These files store the required input information, See SONAR-entrance.Rmd for specific format requirements.
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/result/
These files store the output results.
Proportions of all cell types in each spot (SONAR.results.txt);
Spatial pie plots (pie.pdf);
Spatial distribution of specific cell types proportion (abs_prop.pdf / scaled_prop.pdf);
Colocalization(correlation along the spatial) for pairs of cell types (colocalization.pdf).
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/core-code/
no need to operate.
These files store the core code, and store the preprocessed data that delivered to SONAR.
Please Follow the Example/SONAR-entrance.html or Example/SONAR-entrance.Rmd