AnalysisCSIDE/run_CSIDE/run_de_cer_11.R

In dmcable/RCTD: SpatialeXpressionR: Cell type identification and cell type-specific differential expression in spatial transcriptomics

library(Matrix)
library(spacexr)
library(doParallel)
library(ggplot2)
#source('~/Documents/MIT/Research/Rafalab/Projects/slideseq/Cell Demixing/ContentStructure/RCTD/PersonalFiles/private_utils.R')
#source('~/Documents/MIT/Research/Rafalab/Projects/slideseq/Cell Demixing/ContentStructure/RCTD/de.R')
#source('~/Documents/MIT/Research/Rafalab/Projects/slideseq/Cell Demixing/ContentStructure/RCTD/R/prob_model.R')
#load in RCTD obj
id <- '11'
puck_no <- paste0('190926_', id)
datadir <- paste0('/Users/dcable/Documents/MIT/Research/Rafalab/Projects/slideseq/Cell Demixing/ContentStructure/RCTD/data/SpatialRNA/CerebellumReplicates/Puck_', '190926_11')
resultsdir <- paste0('/Users/dcable/Documents/MIT/Research/Rafalab/Projects/slideseq/Cell Demixing/ContentStructure/RCTD/data/SpatialRNA/CerebellumReplicates/Puck_', puck_no)
myRCTD<- readRDS(file.path(datadir,'myRCTD_cer_reps.rds'))
load(file.path(datadir,"regions.RData"))
explanatory.variable <- c(rep(0,length(nodular_11)), rep(1,length(anterior_11)))#FILL IN
names(explanatory.variable) <- c(nodular_11, anterior_11)
#Check cell types
cell_types = c('Astrocytes','Bergmann','Granule','Purkinje','Oligodendrocytes')
#CSIDE:::aggregate_cell_types(myRCTD, names(explanatory.variable))
#de
puck <- readRDS(file.path(resultsdir, 'puckCropped.rds'))
myRCTD@originalSpatialRNA <- CSIDE:::coerce_old(puck)
colnames(myRCTD@originalSpatialRNA@counts) <- unlist(lapply(colnames(myRCTD@originalSpatialRNA@counts), function(x) paste0(x,'_',id)))
rownames(myRCTD@originalSpatialRNA@coords) <- unlist(lapply(rownames(myRCTD@originalSpatialRNA@coords), function(x) paste0(x,'_',id)))
names(myRCTD@originalSpatialRNA@nUMI) <- unlist(lapply(names(myRCTD@originalSpatialRNA@nUMI), function(x) paste0(x,'_',id)))
myRCTD@config$max_cores <- 2
myRCTD <- run.de.single(myRCTD, explanatory.variable, cell_types = cell_types)

saveRDS(myRCTD,file.path(resultsdir,'myRCTDde.rds'))

#plots
cell_types_present = c('Astrocytes','Bergmann','Granule','Purkinje','MLI1','MLI2','Oligodendrocytes')
make_all_de_plots(myRCTD, resultsdir, cell_types_present = cell_types_present)