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175 changes: 87 additions & 88 deletions LinseedMetadata.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,103 +3,102 @@ library(R6)
LinseedMetadata <- R6Class(
"LinseedMetadata",
public = list(
filtered_samples = NULL,
filtered_dataset = NULL,
V_row = NULL,
V_column = NULL,
raw_dataset = NULL,
path_ = NULL,
analysis_name = NULL,
dataset = NULL,
topGenes = NULL,
cell_types = NULL,
coef_der_X = NULL,
coef_der_Omega = NULL,
coef_hinge_H = NULL,
coef_hinge_W = NULL,
coef_pos_D_h = NULL,
coef_pos_D_w = NULL,
global_iterations = NULL,
init_count_neg_props = NULL,
init_count_neg_basis = NULL,
count_neg_props = NULL,
count_neg_basis = NULL,
filtered_samples = NULL,
filtered_dataset = NULL,
V_row = NULL,
V_column = NULL,
raw_dataset = NULL,
path_ = NULL,
analysis_name = NULL,
dataset = NULL,
topGenes = NULL,
cell_types = NULL,
coef_der_X = NULL,
coef_der_Omega = NULL,
coef_hinge_H = NULL,
coef_hinge_W = NULL,
coef_pos_D_h = NULL,
coef_pos_D_w = NULL,
global_iterations = NULL,
init_count_neg_props = NULL,
init_count_neg_basis = NULL,
count_neg_props = NULL,
count_neg_basis = NULL,

full_proportions = NULL,
full_basis = NULL,
orig_full_proportions = NULL,
orig_full_basis = NULL,
R = NULL,
S = NULL,

final_X = NULL,
final_Omega = NULL,
final_W_ = NULL,
final_H_ = NULL,
final_D_h = NULL,
final_D_w = NULL,

init_D_w = NULL,
init_D_h = NULL,
init_X = NULL,
init_H = NULL,
init_W = NULL,
init_Omega = NULL,
errors_statistics = NULL,
metric = NULL,
full_proportions = NULL,
full_basis = NULL,
orig_full_proportions = NULL,
orig_full_basis = NULL,
R = NULL,
S = NULL,

initialize = function(linseed_object) {
self$filtered_samples <- linseed_object$filtered_samples
self$filtered_dataset <- linseed_object$filtered_dataset
self$raw_dataset <- linseed_object$raw_dataset
self$V_row <- linseed_object$V_row
self$V_column <- linseed_object$V_column
final_X = NULL,
final_Omega = NULL,
final_W_ = NULL,
final_H_ = NULL,
final_D_h = NULL,
final_D_w = NULL,

self$dataset <- linseed_object$dataset
self$path_ <- linseed_object$path_
self$analysis_name <- linseed_object$analysis_name
self$topGenes <- linseed_object$topGenes
self$cell_types <- linseed_object$cell_types
self$coef_der_X <- linseed_object$coef_der_X
self$coef_der_Omega <- linseed_object$coef_der_Omega
self$coef_hinge_H <- linseed_object$coef_hinge_H
self$coef_hinge_W <- linseed_object$coef_hinge_W
self$coef_pos_D_h <- linseed_object$coef_pos_D_h
self$coef_pos_D_w <- linseed_object$coef_pos_D_w
self$global_iterations <- linseed_object$global_iterations
init_D_w = NULL,
init_D_h = NULL,
init_X = NULL,
init_H = NULL,
init_W = NULL,
init_Omega = NULL,
errors_statistics = NULL,
metric = NULL,

self$init_X <- linseed_object$init_X
self$init_Omega <- linseed_object$init_Omega
self$init_H <- linseed_object$init_H
self$init_W <- linseed_object$init_W
initialize = function(linseed_object) {
self$filtered_samples <- linseed_object$filtered_samples
self$filtered_dataset <- linseed_object$filtered_dataset
self$raw_dataset <- linseed_object$raw_dataset
self$V_row <- linseed_object$V_row
self$V_column <- linseed_object$V_column

self$final_X <- linseed_object$X
self$final_Omega <- linseed_object$Omega
self$final_H_ <- linseed_object$H_
self$final_W_ <- linseed_object$W_

self$errors_statistics <- linseed_object$errors_statistics
self$dataset <- linseed_object$dataset
self$path_ <- linseed_object$path_
self$analysis_name <- linseed_object$analysis_name
self$topGenes <- linseed_object$topGenes
self$cell_types <- linseed_object$cell_types
self$coef_der_X <- linseed_object$coef_der_X
self$coef_der_Omega <- linseed_object$coef_der_Omega
self$coef_hinge_H <- linseed_object$coef_hinge_H
self$coef_hinge_W <- linseed_object$coef_hinge_W
self$coef_pos_D_h <- linseed_object$coef_pos_D_h
self$coef_pos_D_w <- linseed_object$coef_pos_D_w
self$global_iterations <- linseed_object$global_iterations

self$R <- linseed_object$R
self$S <- linseed_object$S
self$init_X <- linseed_object$init_X
self$init_Omega <- linseed_object$init_Omega
self$init_H <- linseed_object$init_H
self$init_W <- linseed_object$init_W

self$init_D_h <- linseed_object$init_D_h
self$init_D_w <- linseed_object$init_D_w
self$final_D_h <- linseed_object$D_h
self$final_D_w <- linseed_object$D_w
self$final_X <- linseed_object$X
self$final_Omega <- linseed_object$Omega
self$final_H_ <- linseed_object$H_
self$final_W_ <- linseed_object$W_

self$init_count_neg_props <- linseed_object$init_count_neg_props
self$init_count_neg_basis <- linseed_object$init_count_neg_basis
self$count_neg_props <- linseed_object$count_neg_props
self$count_neg_basis <- linseed_object$count_neg_basis
self$errors_statistics <- linseed_object$errors_statistics

self$full_proportions <- linseed_object$full_proportions
self$orig_full_proportions <- linseed_object$orig_full_proportions
self$full_basis <- linseed_object$full_basis
self$orig_full_basis <- linseed_object$orig_full_basis
self$R <- linseed_object$R
self$S <- linseed_object$S

self$metric <- linseed_object$metric
self$init_D_h <- linseed_object$init_D_h
self$init_D_w <- linseed_object$init_D_w
self$final_D_h <- linseed_object$D_h
self$final_D_w <- linseed_object$D_w

}
)
self$init_count_neg_props <- linseed_object$init_count_neg_props
self$init_count_neg_basis <- linseed_object$init_count_neg_basis
self$count_neg_props <- linseed_object$count_neg_props
self$count_neg_basis <- linseed_object$count_neg_basis

self$full_proportions <- linseed_object$full_proportions
self$orig_full_proportions <- linseed_object$orig_full_proportions
self$full_basis <- linseed_object$full_basis
self$orig_full_basis <- linseed_object$orig_full_basis

self$metric <- linseed_object$metric
}
)
)
131 changes: 65 additions & 66 deletions RunDeconvolution.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -8,12 +8,12 @@ sourceCpp('/app/pipeline.cpp')


option_list <- list(
make_option(c("-c", "--config"), action="store", default=NA, type='character',
help="YAML with configutation path"),
make_option(c("-i", "--init"), action="store", default=NA, type='integer',
help="Initialization number")
make_option(c("-c", "--config"), action = "store", default = NA, type = 'character',
help = "YAML with configutation path"),
make_option(c("-i", "--init"), action = "store", default = NA, type = 'integer',
help = "Initialization number")
)
opt <- parse_args(OptionParser(option_list=option_list))
opt <- parse_args(OptionParser(option_list = option_list))

if (is.na(opt$c)) {
stop("YAML Configuration file path is not specified")
Expand All @@ -30,7 +30,7 @@ dir.create(path_, recursive = T, showWarnings = F)

analysis_name <- obj[['analysis_name']]
if (!is.na(opt$i)) {
analysis_name <- paste0(analysis_name,"_",opt$i)
analysis_name <- paste0(analysis_name, "_", opt$i)
}

if (!is.null(obj[['coef_hinge_H']])) {
Expand Down Expand Up @@ -81,72 +81,71 @@ if (!is.null(obj[['scale_iterations']])) {
scale_iterations <- 20
}

cat(paste("\n",analysis_name,":",
"\nNumber of iterations:",global_iterations,
"\nCell types:",obj[['cell_types']],
"\nDataset:",obj[['dataset']],
"\nPath:",path_,
"\nX derivative coefficient:",coef_der_X,
"\nOmega derivative coefficient:",coef_der_Omega,
"\nSum-to-one D_h coefficient:",coef_pos_D_h,
"\nSum-to-one D_w coefficient:",coef_pos_D_w,
"\nPositive proportions coefficient:",coef_hinge_H,
"\nPositive basis coefficient:",coef_hinge_W,"\n"))
cat(paste("\n", analysis_name, ":",
"\nNumber of iterations:", global_iterations,
"\nCell types:", obj[['cell_types']],
"\nDataset:", obj[['dataset']],
"\nPath:", path_,
"\nX derivative coefficient:", coef_der_X,
"\nOmega derivative coefficient:", coef_der_Omega,
"\nSum-to-one D_h coefficient:", coef_pos_D_h,
"\nSum-to-one D_w coefficient:", coef_pos_D_w,
"\nPositive proportions coefficient:", coef_hinge_H,
"\nPositive basis coefficient:", coef_hinge_W, "\n"))


if (!is.null(obj[['data']])) {
data_ <- readRDS(obj[['data']][['path']])
tmp_snkhrn <- SinkhornNNLSLinseed$new(dataset = obj[['dataset']], path = path_, analysis_name = analysis_name,
cell_types = obj[['cell_types']],
global_iterations = global_iterations,
coef_der_X = coef_der_X, coef_der_Omega = coef_der_Omega,
coef_hinge_H = coef_hinge_H, coef_hinge_W = coef_hinge_W,
coef_pos_D_h = coef_pos_D_h, coef_pos_D_w = coef_pos_D_w,
data = data_)
cell_types = obj[['cell_types']],
global_iterations = global_iterations,
coef_der_X = coef_der_X, coef_der_Omega = coef_der_Omega,
coef_hinge_H = coef_hinge_H, coef_hinge_W = coef_hinge_W,
coef_pos_D_h = coef_pos_D_h, coef_pos_D_w = coef_pos_D_w,
data = data_)
} else {
tmp_snkhrn <- SinkhornNNLSLinseed$new(dataset = obj[['dataset']], path = path_, analysis_name = analysis_name,
cell_types = obj[['cell_types']],
global_iterations = global_iterations,
coef_der_X = coef_der_X, coef_der_Omega = coef_der_Omega,
coef_pos_D_h = coef_pos_D_h, coef_pos_D_w = coef_pos_D_w,
coef_hinge_H = coef_hinge_H, coef_hinge_W = coef_hinge_W)
cell_types = obj[['cell_types']],
global_iterations = global_iterations,
coef_der_X = coef_der_X, coef_der_Omega = coef_der_Omega,
coef_pos_D_h = coef_pos_D_h, coef_pos_D_w = coef_pos_D_w,
coef_hinge_H = coef_hinge_H, coef_hinge_W = coef_hinge_W)
}


tmp_snkhrn$selectTopGenes(min(obj[['top_genes']],nrow(tmp_snkhrn$filtered_data)))

if (!is.null(obj[['svd_k']])) {
k <- max(obj[['cell_types']],obj[['svd_k']])
} else {
k <- obj[['cell_types']]
}

print("Scaling dataset")
tmp_snkhrn$scaleDataset(iterations = scale_iterations)

if (!is.null(obj[['projections']])) {
print("Loading projections")
tmp_snkhrn$readProjections(file = file.path(obj[['projections']][['path']],paste0("ct",tmp_snkhrn$cell_types),paste0(tmp_snkhrn$dataset,"_",opt$i,".rds")))
} else {
print("Get S and R projections")
tmp_snkhrn$getSvdProjectionsNew(k=k)
}


if (!is.null(obj[['inits']])) {
print("Loading initial points")
tmp_snkhrn$readInitValues(file = file.path(obj[['inits']][['path']],paste0("ct",tmp_snkhrn$cell_types),paste0(tmp_snkhrn$dataset,"_",opt$i,".rds")))
} else {
print("Find initial points")
tmp_snkhrn$selectInitOmega()
}

print("Run optimization")
tmp_snkhrn$runOptimization()
print("Save results")
tmp_snkhrn$saveResults()
print("Deconvolution complete")

metadata_ <- LinseedMetadata$new(tmp_snkhrn)
save(metadata_,file=paste0(metadata_$path_,"/",metadata_$analysis_name,".meta"))


tmp_snkhrn$selectTopGenes(min(obj[['top_genes']], nrow(tmp_snkhrn$filtered_data)))

if (!is.null(obj[['svd_k']])) {
k <- max(obj[['cell_types']], obj[['svd_k']])
} else {
k <- obj[['cell_types']]
}

print("Scaling dataset")
tmp_snkhrn$scaleDataset(iterations = scale_iterations)

if (!is.null(obj[['projections']])) {
print("Loading projections")
tmp_snkhrn$readProjections(file = file.path(obj[['projections']][['path']], paste0("ct", tmp_snkhrn$cell_types), paste0(tmp_snkhrn$dataset, "_", opt$i, ".rds")))
} else {
print("Get S and R projections")
tmp_snkhrn$getSvdProjectionsNew(k = k)
}


if (!is.null(obj[['inits']])) {
print("Loading initial points")
tmp_snkhrn$readInitValues(file = file.path(obj[['inits']][['path']], paste0("ct", tmp_snkhrn$cell_types), paste0(tmp_snkhrn$dataset, "_", opt$i, ".rds")))
} else {
print("Find initial points")
tmp_snkhrn$selectInitOmega()
}

print("Run optimization")
tmp_snkhrn$runOptimization()
print("Save results")
tmp_snkhrn$saveResults()
print("Deconvolution complete")

metadata_ <- LinseedMetadata$new(tmp_snkhrn)
save(metadata_, file = paste0(metadata_$path_, "/", metadata_$analysis_name, ".meta"))
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