RETROFIT enables reference-free cell-type deconvolution of spatial transcriptomics data.

Installation

Install retrofit from github:

install.packages("devtools") 
devtools::install_github("qunhualilab/retrofit")

Install retrofit from Bioconductor.

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

BiocManager::install(version='devel')
BiocManager::install("retrofit")

Example

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
• Colon Vignette