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RCTD_helper.R
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#decompose with just two cell types
#if score_mode, then returns the objective function score
#if denoise, then it fits a "noise" dimension as the mean of all the data
decompose_sparse <- function(cell_type_profiles, nUMI, bead, type1=NULL, type2=NULL, score_mode = FALSE, plot = F, custom_list = NULL, verbose=F, constrain = T, MIN.CHANGE = 0.001) {
if(is.null(custom_list))
cell_types = c(type1,type2)
else
cell_types = custom_list
reg_data = data.matrix(cell_type_profiles[,cell_types])
if(score_mode)
n.iter = 25
else
n.iter = 50
results = solveIRWLS.weights(reg_data,bead,nUMI,OLS = FALSE, constrain = constrain, verbose = verbose, n.iter = n.iter, MIN_CHANGE = MIN.CHANGE)
if(! score_mode) {
results$weights = results$weights / sum(results$weights)
return(results)
} else {
prediction = reg_data %*% results$weights
total_score = calc_log_l_vec(prediction, bead)
return (total_score)
}
}
#decompose with all cell types
decompose_full <- function(cell_type_profiles, nUMI, bead, constrain = TRUE, OLS = FALSE, verbose = F, n.iter = 50, MIN_CHANGE = 0.001, bulk_mode = F) {
results = solveIRWLS.weights(cell_type_profiles,bead,nUMI,OLS = OLS, constrain = constrain,
verbose = verbose, n.iter = n.iter, MIN_CHANGE = MIN_CHANGE, bulk_mode = bulk_mode)
return(results)
}
check_pairs_type <- function(cell_type_profiles, bead, UMI_tot, score_mat, min_score, my_type, class_df, QL_score_cutoff, constrain, singlet_scores, MIN.CHANGE = 0.001) {
candidates = rownames(score_mat)
singlet_score = singlet_scores[my_type]
all_pairs = T; all_pairs_class = !is.null(class_df)
other_class = my_type #other types present from this class
for(i in 1:(length(candidates)-1)) {
type1 = candidates[i]
for(j in (i+1):length(candidates)) {
type2 = candidates[j]
if(score_mat[i,j] < min_score + QL_score_cutoff) {
if(type1 != my_type && type2 != my_type)
all_pairs = F
if(!is.null(class_df)) {
first_class = class_df[my_type,"class"] == class_df[type1,"class"]
second_class = class_df[my_type,"class"] == class_df[type2,"class"]
if(!first_class && !second_class)
all_pairs_class = F
if(first_class && ! (type1 %in% other_class))
other_class = c(other_class, type1)
if(second_class && ! (type2 %in% other_class))
other_class = c(other_class, type2)
}
}
}
}
if(is.null(class_df))
all_pairs_class = all_class
if(all_pairs_class && !all_pairs && length(other_class) > 1) {
for (type in other_class[2:length(other_class)])
singlet_score = min(singlet_score, singlet_scores[type])
}
return(list(all_pairs = all_pairs, all_pairs_class = all_pairs_class, singlet_score = singlet_score))
}
#Decomposing a single bead via doublet search
process_bead_doublet <- function(cell_type_info, gene_list, UMI_tot, bead, class_df = NULL, constrain = T, verbose = F,
MIN.CHANGE = 0.001, CONFIDENCE_THRESHOLD = 10, DOUBLET_THRESHOLD = 25) {
cell_type_profiles <- cell_type_info[[1]][gene_list,]
cell_type_profiles = cell_type_profiles * UMI_tot
cell_type_profiles = data.matrix(cell_type_profiles)
QL_score_cutoff = CONFIDENCE_THRESHOLD; doublet_like_cutoff = DOUBLET_THRESHOLD
results_all = decompose_full(cell_type_profiles, UMI_tot, bead, constrain = constrain, verbose = verbose, MIN_CHANGE = MIN.CHANGE)
all_weights <- results_all$weights
conv_all <- results_all$converged
initial_weight_thresh = 0.01; cell_type_names = cell_type_info[[2]]
candidates <- names(which(all_weights > initial_weight_thresh))
if(length(candidates) == 0)
candidates = cell_type_info[[2]][1:min(3,cell_type_info[[3]])]
if(length(candidates) == 1)
if(candidates[1] == cell_type_info[[2]][1])
candidates = c(candidates, cell_type_info[[2]][2])
else
candidates = c(candidates, cell_type_info[[2]][1])
score_mat = Matrix(0, nrow = length(candidates), ncol = length(candidates))
rownames(score_mat) = candidates; colnames(score_mat) = candidates
singlet_scores <- numeric(length(candidates))
names(singlet_scores) <- candidates
for(type in candidates) {
singlet_scores[type] <- get_singlet_score(cell_type_profiles, bead, UMI_tot,
type, constrain, MIN.CHANGE = MIN.CHANGE)
}
min_score = 0
first_type = NULL; second_type = NULL
first_class = F; second_class = F #indicates whether the first (resp second) refers to a class rather than a type
for(i in 1:(length(candidates)-1)) {
type1 = candidates[i]
for(j in (i+1):length(candidates)) {
type2 = candidates[j]
score = decompose_sparse(cell_type_profiles, UMI_tot, bead, type1, type2, score_mode = T, constrain = constrain, verbose = verbose, MIN.CHANGE = MIN.CHANGE)
score_mat[i,j] = score; score_mat[j,i] = score
if(is.null(second_type) || score < min_score) {
first_type <- type1; second_type <- type2
min_score = score
}
}
}
type1_pres = check_pairs_type(cell_type_profiles, bead, UMI_tot, score_mat, min_score, first_type, class_df, QL_score_cutoff, constrain, singlet_scores, MIN.CHANGE = MIN.CHANGE)
type2_pres = check_pairs_type(cell_type_profiles, bead, UMI_tot, score_mat, min_score, second_type, class_df, QL_score_cutoff, constrain, singlet_scores, MIN.CHANGE = MIN.CHANGE)
if(!type1_pres$all_pairs_class && !type2_pres$all_pairs_class) {
spot_class <- "reject"
singlet_score = min_score + 2 * doublet_like_cutoff #arbitrary
}
else if(type1_pres$all_pairs_class && !type2_pres$all_pairs_class) {
first_class <- !type1_pres$all_pairs
singlet_score = type1_pres$singlet_score
spot_class = "doublet_uncertain"
} else if(!type1_pres$all_pairs_class && type2_pres$all_pairs_class) {
first_class <- !type2_pres$all_pairs
singlet_score = type2_pres$singlet_score
temp = first_type; first_type = second_type; second_type = temp
spot_class = "doublet_uncertain"
} else {
spot_class = "doublet_certain"
singlet_score = min(type1_pres$singlet_score, type2_pres$singlet_score)
first_class <- !type1_pres$all_pairs; second_class <- !type2_pres$all_pairs
if(type2_pres$singlet_score < type1_pres$singlet_score) {
temp = first_type; first_type = second_type; second_type = temp
first_class <- !type2_pres$all_pairs; second_class <- !type1_pres$all_pairs
}
}
if(singlet_score - min_score < doublet_like_cutoff)
spot_class = "singlet"
doublet_results = decompose_sparse(cell_type_profiles, UMI_tot, bead, first_type, second_type, constrain = constrain, MIN.CHANGE = MIN.CHANGE)
doublet_weights = doublet_results$weights; conv_doublet = doublet_results$converged
spot_class <- factor(spot_class, c("reject", "singlet", "doublet_certain", "doublet_uncertain"))
return(list(all_weights = all_weights, spot_class = spot_class, first_type = first_type, second_type = second_type,
doublet_weights = doublet_weights, min_score = min_score, singlet_score = singlet_score,
conv_all = conv_all, conv_doublet = conv_doublet, score_mat = score_mat, singlet_scores = singlet_scores,
first_class = first_class, second_class = second_class))
}
#Decomposing a single bead via doublet search
process_bead_multi <- function(cell_type_info, gene_list, UMI_tot, bead, class_df = NULL, constrain = T, verbose = F,
MIN.CHANGE = 0.001, MAX.TYPES = 4, CONFIDENCE_THRESHOLD = 10, DOUBLET_THRESHOLD = 25) {
cell_type_profiles <- cell_type_info[[1]][gene_list,]
cell_type_profiles = cell_type_profiles * UMI_tot
cell_type_profiles = data.matrix(cell_type_profiles)
QL_score_cutoff = CONFIDENCE_THRESHOLD; doublet_like_cutoff = DOUBLET_THRESHOLD
results_all = decompose_full(cell_type_profiles, UMI_tot, bead, constrain = constrain, verbose = verbose, MIN_CHANGE = MIN.CHANGE)
all_weights <- results_all$weights
conv_all <- results_all$converged
initial_weight_thresh = 0.01; cell_type_names = cell_type_info[[2]]
candidates <- names(which(all_weights > initial_weight_thresh))
if(length(candidates) == 0)
stop('process_bead_multi: no cell types passed weight threshold on full mode. Please check that enough counts are present for each pixel')
cell_type_list <- c()
curr_score <- 10000000000
for(n in 1:MAX.TYPES) {
min_score = curr_score
best_type = NULL
for(type in candidates) {
cur_list <- c(cell_type_list, type)
score = decompose_sparse(cell_type_profiles, UMI_tot, bead, custom_list = cur_list, score_mode = T,
constrain = constrain, verbose = verbose, MIN.CHANGE = MIN.CHANGE)
if(score < min_score) {
best_type = type
min_score = score
}
}
if(min_score > curr_score - doublet_like_cutoff) {
break; # don't add new cell type
} else {
cell_type_list <- c(cell_type_list, best_type)
candidates <- setdiff(candidates, best_type)
curr_score <- min_score
}
}
#check for confidence
conf_list <- !logical(length(cell_type_list)); names(conf_list) = cell_type_list
for(type in cell_type_list)
for(newtype in candidates) {
cur_list <- c(setdiff(cell_type_list,type), newtype)
score = decompose_sparse(cell_type_profiles, UMI_tot, bead, custom_list = cur_list, score_mode = T,
constrain = constrain, verbose = verbose, MIN.CHANGE = MIN.CHANGE)
if(score < curr_score + QL_score_cutoff) {
conf_list[type] = FALSE
break;
}
}
#get final weights
sub_results = decompose_sparse(cell_type_profiles, UMI_tot, bead, custom_list = cell_type_list, score_mode = F,
constrain = constrain, verbose = verbose, MIN.CHANGE = MIN.CHANGE)
sub_weights = sub_results$weights; conv_sub = sub_results$converged
return(list(all_weights = all_weights, cell_type_list = cell_type_list, conf_list = conf_list,
sub_weights = sub_weights, min_score = curr_score,
conv_all = conv_all, conv_sub = conv_sub))
}
get_prediction_sparse <- function(cell_type_profiles, UMI_tot, p, type1, type2) {
cell_types = c(type1,type2)
reg_data = cell_type_profiles[,cell_types]
prediction = reg_data %*% c(p,1-p)
return(prediction)
}
get_singlet_score <- function(cell_type_profiles, bead, UMI_tot, type, constrain, MIN.CHANGE = 0.001, return_vec = FALSE) {
if(!constrain)
return(decompose_sparse(cell_type_profiles, UMI_tot, bead, type1=type, score_mode = T, constrain = constrain, MIN.CHANGE = MIN.CHANGE))
dummy_type = colnames(cell_type_profiles)[1]
if(dummy_type == type)
dummy_type = colnames(cell_type_profiles)[2]
prediction <- get_prediction_sparse(cell_type_profiles, UMI_tot, 1, type, dummy_type)
log_l <- calc_log_l_vec(prediction, bead, return_vec = return_vec)
return(log_l)
}
#decompose a doublet into two cells
decompose_doublet_fast <- function(bead, weights, gene_list, cell_type_info, type1, type2) {
N_genes = length(gene_list)
expect_1 = vector(mode="numeric",length = N_genes)
expect_2 = vector(mode="numeric",length = N_genes)
variance = vector(mode="numeric",length = N_genes)
names(expect_1) = gene_list; names(expect_2) = gene_list; names(variance) = gene_list
epsilon = 1e-10
for(ind in which(bead > 0)) {
gene = gene_list[ind]
denom = weights[1] * cell_type_info[[1]][gene,type1] + weights[2] * cell_type_info[[1]][gene,type2] + epsilon
posterior_1 = (weights[1] * cell_type_info[[1]][gene,type1] + epsilon / 2) / denom
expect_1[[ind]] = posterior_1 * bead[gene]
expect_2[[ind]] = bead[gene] - posterior_1 * bead[gene]
variance[[ind]] = posterior_1 * bead[gene] * (1 - posterior_1)
}
return(list(expect_1 = expect_1, expect_2 = expect_2, variance = variance))
}