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Fix multiomics normalization at upload #1621

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Merged
merged 3 commits into from
Nov 11, 2025
Merged

Fix multiomics normalization at upload #1621

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983ac92
fix normalization for multiomics
zitoa Nov 11, 2025
69ee228
use new playbase functions
zitoa Nov 11, 2025
dd9b923
use sub
zitoa Nov 11, 2025
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21 changes: 10 additions & 11 deletions components/board.upload/R/upload_module_normalization.R
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Original file line number Diff line number Diff line change
Expand Up @@ -71,15 +71,16 @@ upload_module_normalization_server <- function(

is.multiomics <- playbase::is.multiomics(rownames(counts))
if (is.multiomics) {
## Scaled log1p transform with autoscaling on non-zero quantile.
## Only applied to multi-omics. It also performs median scaling.
X <- playbase::mofa.log1s(counts, q = 0.20)
prior <- 0
} else {
prior0 <- 0
if (min(counts, na.rm = TRUE) == 0 || any(is.na(counts))) {
prior0 <- min(counts[counts > 0], na.rm = TRUE)
X <- counts
dtypes <- unique(sub(":.*", "", rownames(X)))
for(i in 1:length(dtypes)) {
ii <- grep(paste0("^", dtypes[i], ":"), rownames(counts))
prior <- 1
if (dtypes[i] != "gx") prior <- playbase::getPrior(counts[ii, ])
X[ii, ] <- log2(counts[ii, ] + prior)
}
} else {
prior0 <- playbase::getPrior(counts)
m <- input$normalization_method
prior <- ifelse(grepl("CPM|TMM", m), 1, prior0)
X <- log2(counts + prior)
Expand All @@ -88,7 +89,6 @@ upload_module_normalization_server <- function(
dbg("[normalization_server:imputedX] X has ", sum(is.na(X)), " missing values (NAs).")
dbg("[normalization_server:imputedX] X has ", sum(rowSums(is.na(X)) > 0), " rows with NAs.")


## Filter probes for maximum missingness as required
if (sum(is.na(X)) > 0 && input$filtermissing) {
f <- input$filterthreshold
Expand Down Expand Up @@ -140,8 +140,7 @@ upload_module_normalization_server <- function(
shiny::req(ref)
}
if (upload_datatype() == "multi-omics") {
dbg("[normalization_server:normalizedX] normalizing MultOmics data using ", m)
X <- playbase::normalizeMultiOmics(X, method = m) ## unneeded: done in mofa.log1s.
X <- playbase::normalizeMultiOmics(X)
} else {
dbg("[normalization_server:normalizedX] normalizing data using ", m)
X <- playbase::normalizeExpression(X, method = m, ref = ref, prior = prior)
Expand Down
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