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fix a bug in generatePortalInputs: the networks.txt contains quotes
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@QingfeiPan
QingfeiPan committed Aug 8, 2024
1 parent 351d7f8 commit 32bc9b2
Showing 1 changed file with 38 additions and 15 deletions.
53 changes: 38 additions & 15 deletions R/visualization.R
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Original file line number Diff line number Diff line change
Expand Up @@ -697,8 +697,8 @@ generatePortalInputs <- function(input_expression.eset = NULL,
}

## prepare expression data
if (is.null(input_expression.eset)) {
if (is.null(input_expression.seuratObj)) {
if (is.null(input_expression.eset) == TRUE) {
if (is.null(input_expression.seuratObj) == TRUE) {
cat("The expression data preparation for scMINER Portal has been skipped, since no inputs was provided.\n")
} else {
cat("The expression data for scMINER Portal will be prepared from the input Seurat object...\n")
Expand All @@ -725,7 +725,13 @@ generatePortalInputs <- function(input_expression.eset = NULL,
# meta data
cat("\tChecking the meta.data ...")
seurat_metadata <- data.frame(CellID = row.names(input_expression.seuratObj@meta.data), input_expression.seuratObj@meta.data, CellGroup = Seurat::Idents(input_expression.seuratObj))
if (is.null(group_by) == FALSE) {seurat_metadata[, "CellGroup"] <- seurat_metadata[, group_by]}
if (is.null(group_by) == FALSE) {
if (group_by %in% colnames(seurat_metadata)) {
seurat_metadata[, "CellGroup"] <- seurat_metadata[, group_by]
} else {
stop("The group_by was not found in meta.data. Please check and re-try.")
}
}
cat("\t\tDone! The meta.data are ready.\n")

# expression matrix
Expand All @@ -750,6 +756,7 @@ generatePortalInputs <- function(input_expression.eset = NULL,

## check pheno data
pd <- Biobase::pData(input_expression.eset)
if (("CellID" %in% colnames(pd)) == FALSE) {pd$CellID <- row.names(pd)}

cat("\tChecking the reduction results ...")
reductions_col <- grepl("umap|tsne", colnames(pd), ignore.case = TRUE)
Expand All @@ -761,20 +768,24 @@ generatePortalInputs <- function(input_expression.eset = NULL,

cat("\tChecking the group info ...")
if (is.null(group_by) == FALSE) {
pd[, "CellGroup"] <- pd[, group_by]
if (group_by %in% colnames(pd)) {
pd[, "CellGroup"] <- pd[, group_by]
} else {
stop("The group_by was not found in input eset object. Please check and re-try.")
}
cat("\t\tDone! The CellGroup column had been set by:", group_by, ".\n")
} else {
if ("clusterID" %in% colnames(pd)) {
pd[, "CellGroup"] <- pd[, "clusterID"]
cat("\t\tDone! The CellGroup column had been set by: clusterID.\n")
cat("\t\tDone! The 'group_by' is not specified and the default value is used: 'clusterID'. To change it, please specify 'group_by' argument.\n")
} else {
stop('Please specify "group_by" to define the group info.')
}
}

expression.eset <- updateSparseEset(input_expression.eset, cellData = pd, addMetaData = FALSE)
saveRDS(expression.eset, file = paste0(output_dir, "/expression.eset"))
cat("The expression data for scMINER Portal has been generated:", paste0(output_dir, "/expression.eset"),".\n")
saveRDS(expression.eset, file = paste0(output_dir, "/expression.rds"))
cat("The expression data for scMINER Portal has been generated:", paste0(output_dir, "/expression.rds"),".\n")
} else {
stop('Please use ONLY ONE of "input_expression.eset" or "input_expression.seuratObj" to specify the input expression data.')
}
Expand All @@ -784,6 +795,12 @@ generatePortalInputs <- function(input_expression.eset = NULL,
if (is.null(input_activity.eset) == FALSE) {
cat("The activity data for scMINER Portal will be prepared from the input eset object ...\n")

fd <- Biobase::fData(input_activity.eset)
if (("GeneSymbol" %in% colnames(fd)) == FALSE) {fd$GeneSymbol <- gsub("[_TF|_SIG]", "", row.names(fd))}

pd <- Biobase::pData(input_activity.eset)
if (("CellID" %in% colnames(pd)) == FALSE) {pd$CellID <- row.names(pd)}

cat("\tChecking the reduction results ...")
reductions_col <- grepl("umap|tsne", colnames(pd), ignore.case = TRUE)
if (length(reductions_col) > 0) {
Expand All @@ -794,7 +811,11 @@ generatePortalInputs <- function(input_expression.eset = NULL,

cat("\tChecking the group info ...")
if (is.null(group_by) == FALSE) {
pd[, "CellGroup"] <- pd[, group_by]
if (group_by %in% colnames(pd)) {
pd[, "CellGroup"] <- pd[, group_by]
} else {
stop("The group_by was not found in input eset object. Please check and re-try.")
}
cat("\t\tDone! The CellGroup column had been set by:", group_by, ".\n")
} else {
if ("clusterID" %in% colnames(pd)) {
Expand All @@ -805,9 +826,9 @@ generatePortalInputs <- function(input_expression.eset = NULL,
}
}

activity.eset <- updateSparseEset(input_expression.eset, cellData = pd, addMetaData = FALSE)
saveRDS(activity.eset, file = paste0(output_dir, "/activity.eset"))
cat("The activity data for scMINER Portal has been generated:", paste0(output_dir, "/activity.eset"),".\n")
activity.eset <- updateSparseEset(input_activity.eset, cellData = pd, featureData = fd, addMetaData = FALSE)
saveRDS(activity.eset, file = paste0(output_dir, "/activity.rds"))
cat("The activity data for scMINER Portal has been generated:", paste0(output_dir, "/activity.rds"),".\n")
} else {
cat("The activity data preparation for scMINER Portal has been skipped, since no inputs was provided.\n")
}
Expand All @@ -826,7 +847,7 @@ generatePortalInputs <- function(input_expression.eset = NULL,
network_merged <- data.frame()
for (i in 1:length(grps)) {
dir.tmp <- paste0(input_network.dir, "/", grps[i])
network.tf <- list.files(path = paste0(dir.tmp, "/TF"), pattern="consensus_network_ncol_.txt", recursive = TRUE, full.names = TRUE)
network.tf <- list.files(path = paste0(dir.tmp, "/TF"), pattern = "consensus_network_ncol_.txt", recursive = TRUE, full.names = TRUE)
if (length(network.tf) == 1) {
net.tf <- read.delim(file = network.tf, stringsAsFactors = FALSE)
net.tf$CellGroup <- grps[i]; net.tf$NetworkType <- "TF";
Expand All @@ -835,7 +856,8 @@ generatePortalInputs <- function(input_expression.eset = NULL,
} else {
stop('Multiple TF network files were found for group:', grps[i], '.')
}
network.sig <- list.files(path = paste0(dir.tmp, "/SIG"), pattern="consensus_network_ncol_.txt", recursive = TRUE, full.names = TRUE)

network.sig <- list.files(path = paste0(dir.tmp, "/SIG"), pattern = "consensus_network_ncol_.txt", recursive = TRUE, full.names = TRUE)
if (length(network.sig) == 1) {
net.sig <- read.delim(file = network.sig, stringsAsFactors = FALSE)
net.sig$CellGroup <- grps[i]; net.sig$NetworkType <- "SIG";
Expand All @@ -844,12 +866,13 @@ generatePortalInputs <- function(input_expression.eset = NULL,
} else {
stop('Multiple SIG network files were found for group:', grps[i], '.')
}

network.grp <- rbind(net.tf, net.sig)

if (i == 1) {network_merged <- network.grp} else {network_merged <- rbind(network_merged, network.grp)}
}

write.table(network_merged, file = paste0(output_dir, "/networks.txt"))
write.table(network_merged, file = paste0(output_dir, "/networks.txt"), quote = FALSE, col.names = TRUE, row.names = FALSE, sep = "\t")
cat("The network data for scMINER Portal has been generated:", paste0(output_dir, "/networks.txt"),".\n")
}
} else {
Expand Down Expand Up @@ -880,7 +903,7 @@ generatePortalInputs <- function(input_expression.eset = NULL,
if (i == 1) {network_merged <- net.tmp} else {network_merged <- rbind(network_merged, net.tmp)}
}

write.table(network_merged, file = paste0(output_dir, "/networks.txt"))
write.table(network_merged, file = paste0(output_dir, "/networks.txt"), quote = FALSE, col.names = TRUE, row.names = FALSE, sep = "\t")
cat("The network data for scMINER Portal has been generated:", paste0(output_dir, "/networks.txt"),".\n")
} else {
cat("The network data preparation for scMINER Portal has been skipped, since no inputs was provided.\n")
Expand Down

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