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fix: check dimensions of DEG markers vs number of cells #8

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Merged
rroutsong merged 1 commit into from
Jun 5, 2026
Merged

fix: check dimensions of DEG markers vs number of cells #8

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22 changes: 22 additions & 0 deletions R/makeShinyFilesDEG.R
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Original file line number Diff line number Diff line change
Expand Up @@ -121,6 +121,28 @@ makeShinyFilesDEG <- function(
)
}

# Validate DEG cluster levels match metadata cluster levels
deg_clusters <- sort(unique(as.character(markergenes$cluster)))
meta_clusters <- sort(unique(as.character(obj@meta.data[[clusters]])))
if (!all(deg_clusters %in% meta_clusters)) {
missing <- setdiff(deg_clusters, meta_clusters)
stop(
"DEG markers contain cluster(s) not found in metadata column '", clusters, "': ",
paste(missing, collapse = ", "),
"\n DEG clusters: ", paste(deg_clusters, collapse = ", "),
"\n Metadata clusters: ", paste(meta_clusters, collapse = ", ")
)
}

# Validate that the clusters column exists in scConf (i.e. it was not filtered out)
if (!clusters %in% scConf$ID && !clusters %in% scConf$UI) {
stop(
"Cluster label '", clusters, "' was not included in the ShinyCell config (sc1conf). ",
"It may have been removed by metadata filtering (rmmeta/unsupported assay pattern). ",
"Please ensure this column is retained in the config."
)
}

# markergene h5 creation
n_rows <- nrow(markergenes)
n_cols <- ncol(markergenes)
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4 changes: 2 additions & 2 deletions R/writer1.R
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Expand Up @@ -131,8 +131,8 @@ wrSVmainA1 <- function(prefix) {
' return(list(res,resDef,resLen))\n',
' }})\n',
' observeEvent(gsub("^Assay: ", "", input${prefix}a1ass1), {{\n',
' updateSelectizeInput(session, "{prefix}a1inp1", choices = getG{prefix}a1inp1()[[1]], \n',
' server = TRUE, selected = getG{prefix}a1inp1()[[2]], options = list( \n',
' updateSelectizeInput(session, "{prefix}a1inp1", choices = getG{prefix}a1inp1()[[1]], \n',
' server = TRUE, selected = getG{prefix}a1inp1()[[1]][1], options = list( \n',
' maxOptions = getG{prefix}a1inp1()[[3]], create = TRUE, \n',
' persist = TRUE, render = I(optCrt))) \n',
' }})\n',
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4 changes: 3 additions & 1 deletion R/writer2.R
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Expand Up @@ -149,7 +149,9 @@ wrUImainA1 <- function(prefix, ptsiz) {
' selectInput("{prefix}a1ass1", "Data type to colour plot:",\n',
' choices = c("Cell Information", paste0("Assay: ", {prefix}def$assay)), \n',
' selected = "Cell Information"), \n',
' selectInput("{prefix}a1inp1", "Cell Info / Feature Name:", choices = NULL) %>% \n',
' selectInput("{prefix}a1inp1", "Cell Info / Feature Name:", \n',
' choices = {prefix}conf$UI, \n',
' selected = {prefix}conf$UI[1]) %>% \n',
' helper(type = "inline", size = "m", fade = TRUE,\n',
' title = "Cell Info / Gene to colour cells by",\n',
' content = c("Select cell info / feature to colour cells",\n',
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