RETROFIT enables reference-free cell-type deconvolution of spatial transcriptomics data.
##
 <br />
## Installation
Install `retrofit` from github:
``` r
install.packages("devtools")
devtools::install_github("qunhualilab/retrofit")
```
Install `retrofit` from [Bioconductor](https://bioconductor.org/packages/devel/bioc/html/retrofit.html).
```{r}
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(version='devel')
BiocManager::install("retrofit")
```
## Example
``` r
library(retrofit)
## load built in data
data(testSimulationData)
x = testSimulationData$extra5_x
sc_ref = testSimulationData$sc_ref
marker_ref = testSimulationData$marker_ref
## decompose
res = retrofit::decompose(x, L=16, iterations=100, verbose=TRUE)
W = res$w
H = res$h
TH = res$th
## annotate with correlations
res = retrofit::annotateWithCorrelations(sc_ref, K=8, decomp_w=W, decomp_h=H)
W_annotated = res$w
H_annotated = res$h
cells = res$ranked_cells
## annotate with markers
res = retrofit::annotateWithMarkers(marker_ref, K=8, decomp_w=W, decomp_h=H)
W_annotated = res$w
H_annotated = res$h
cells = res$ranked_cells
```
More details can be found in the vignettes.
- [Simulation Vignette](https://github.com/qunhualilab/retrofit/blob/main/vignettes/SimulationVignette.Rmd)
- [Colon Vignette](https://github.com/qunhualilab/retrofit/blob/main/vignettes/ColonVignette.Rmd)
