Continue update logging to CLI form

NAMESPACE

@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method("[",liger)
 S3method("[",ligerDataset)
 S3method("[[",liger)
 S3method(.DollarNames,liger)
@@ -189,7 +190,6 @@ exportClasses(ligerRNADataset)
 exportClasses(ligerSpatialDataset)
 exportMethods("$")
 exportMethods("$<-")
-exportMethods("[")
 exportMethods("cellMeta<-")
 exportMethods("coordinate<-")
 exportMethods("dataset<-")

R/ATAC.R

@@ -50,12 +50,6 @@ imputeKNN <- function(
         knn_k = nNeighbors
 ) {
     .deprecateArgs(list(knn_k = "nNeighbors"), defunct = "scale")
-    # if (!requireNamespace("FNN", quietly = TRUE)) {
-    #     stop("Package \"foreach\" needed for this function to work. ",
-    #          "Please install it by command:\n",
-    #          "install.packages('FNN')",
-    #          call. = FALSE)
-    # }
     if (is.null(getMatrix(object, "H.norm")))
         cli::cli_abort(
             "Aligned factor loading has to be available for imputation.

R/DEG_marker.R

@@ -96,7 +96,7 @@ runPairwiseDEG <- function(
         groups <- list(group1Idx, group2Idx)
         names(groups) <- c(group1Name, group2Name)
     } else {
-        stop("Please see `?runPairwiseDEG` for usage.")
+        cli::cli_abort("Please see {.code ?runPairwiseDEG} for usage.")
     }
     result <- .runDEG(object, groups = groups, method = method,
                       usePeak = usePeak, useReplicate = useReplicate,
@@ -161,7 +161,7 @@ runMarkerDEG <- function(
     allCellIdx <- seq(ncol(object))[object$dataset %in% useDatasets]
     conditionBy <- conditionBy %||% object@uns$defaultCluster
     if (is.null(conditionBy)) {
-        stop("No `conditionBy` given or default cluster not set.")
+        cli::cli_abort("No {.var conditionBy} given or default cluster not set.")
     }
     conditionBy <- .fetchCellMetaVar(
         object, conditionBy, cellIdx = allCellIdx,
@@ -241,6 +241,8 @@ runWilcoxon <- function(
 ) {
     method <- match.arg(method)
     allCellIdx <- unlist(groups)
+    if (length(allCellIdx) == 0)
+        cli::cli_abort(c(x = "No cell selected"))
     allCellBC <- colnames(object)[allCellIdx]
     datasetInvolve <- levels(object$dataset[allCellIdx, drop = TRUE])
     var <- factor(rep(names(groups), lengths(groups)), levels = names(groups))
@@ -258,8 +260,10 @@ runWilcoxon <- function(
     mat <- Reduce(cbind, dataList)
     mat <- mat[, allCellBC, drop = FALSE]
     if (method == "wilcoxon") {
+        cliID <- cli::cli_process_start("Running Wilcoxon rank-sum test")
         mat <- log1p(1e10*mat)
         result <- wilcoxauc(mat, var)
+        cli::cli_process_done(id = cliID)
     } else if (method == "pseudoBulk") {
         if (is.null(useReplicate)) {
             replicateAnn <- setupPseudoRep(var, nRep = nPsdRep,
@@ -292,27 +296,31 @@ runWilcoxon <- function(
 
 .DE.checkDataAvail <- function(object, useDatasets, method, usePeak) {
     if (isH5Liger(object, useDatasets)) { # nocov start
-        stop("HDF5 based datasets detected but is not supported. \n",
-             "Try `object.sub <- downsample(object, useSlot = ",
-             "'normData')` to create ANOTHER object with in memory data.")
+        cli::cli_abort(
+            c("HDF5 based datasets detected but is not supported. ",
+              "i" = "Try {.code object.sub <- downsample(object, useSlot = 'normData')} to create another object with in memory data")
+        )
     } # nocov end
     if (method == "wilcoxon") {
         slot <- ifelse(usePeak, "normPeak", "normData")
     } else if (method == "pseudoBulk") {
         if (!requireNamespace("DESeq2", quietly = TRUE)) # nocov start
-            stop("Package \"DESeq2\" needed for this function to work. ",
-                 "Please install it by command:\n",
-                 "BiocManager::install('DESeq2')",
-                 call. = FALSE) # nocov end
+            cli::cli_abort(
+                "Package {.pkg DESeq2} is needed for this function to work.
+                Please install it by command:
+                {.code BiocManager::install('DESeq2')}"
+            ) # nocov end
         slot <- ifelse(usePeak, "rawPeak", "rawData")
     }
     allAvail <- all(sapply(useDatasets, function(d) {
         ld <- dataset(object, d)
         !is.null(methods::slot(ld, slot))
     }))
     if (!allAvail)
-        stop(slot, " not all available for involved datasets. [method = \"",
-             method, "\", usePeak = ", usePeak, "]")
+        cli::cli_abort(
+            c("{.field {slot}} not all available for involved datasets: {.val {useDatasets}}",
+              "i" = "{.code method = '{method}'}; {.code usePeak = {usePeak}}")
+        )
     return(slot)
 }
 
@@ -345,9 +353,10 @@ makePseudoBulk <- function(mat, replicateAnn, minCellPerRep, verbose = TRUE) {
         subrep <- replicateAnn[replicateAnn$groups == gr,]
         splitLabel <- interaction(subrep, drop = TRUE)
         if (nlevels(splitLabel) < 2) {
-            stop("Too few replicates label for condition \"", gr, "\". ",
-                 "Cannot not create pseudo-bulks. Please use ",
-                 "consider creating pseudo-replicates or use wilcoxon instead.")
+            cli::cli_abort(
+                c("Too few replicates for condition {.val {gr}}. Cannot create pseudo-bulks.",
+                  "i" = "Please consider creating pseudo-replicates or using {.code method = 'wilcoxon'} instead.")
+            )
         }
     }
     splitLabel <- interaction(replicateAnn, drop = TRUE)
@@ -360,10 +369,9 @@ makePseudoBulk <- function(mat, replicateAnn, minCellPerRep, verbose = TRUE) {
     mat <- mat[, idx, drop = FALSE]
     replicateAnn <- replicateAnn[idx, , drop = FALSE]
     if (verbose) {
-        .log("Ignoring replicates with too few cells: ",
-             paste0(ignored, collapse = ", "))
-        .log("Replicate size:")
-        .log(paste0(levels(splitLabel), ": ", table(splitLabel), collapse = ", "), level = 2)
+        if (length(ignored) > 0) cli::cli_alert_warning("Ignoring replicates with too few cells: {.val {ignored}}")
+        cli::cli_alert_info("Replicate sizes:")
+        print(table(splitLabel))
     }
     pseudoBulks <- colAggregateSums_sparse(mat, as.integer(splitLabel) - 1,
                                            nlevels(splitLabel))
@@ -375,7 +383,7 @@ makePseudoBulk <- function(mat, replicateAnn, minCellPerRep, verbose = TRUE) {
 .callDESeq2 <- function(pseudoBulks, groups,
                          verbose = getOption("ligerVerbose")) {
     # DESeq2 workflow
-    if (isTRUE(verbose)) .log("Calling DESeq2 Wald test")
+    if (isTRUE(verbose)) cliID <- cli::cli_process_start("Calling DESeq2 Wald test")
     ## NOTE: DESeq2 wishes that the contrast/control group is the first level
     ## whereas we required it as the second in upstream input. So we need to
     ## reverse it here.
@@ -396,6 +404,7 @@ makePseudoBulk <- function(mat, replicateAnn, minCellPerRep, verbose = TRUE) {
     res$group <- levels(groups)[2]
     res <- res[, c(7, 8, 2, 5, 6)]
     colnames(res) <- c("feature", "group", "logFC", "pval", "padj")
+    if (isTRUE(verbose)) cli::cli_process_done(id = cliID)
     return(res)
 }
 

R/DoubletFinder.R

@@ -41,27 +41,29 @@ runDoubletFinder <- function(
         ...
 ) {
     if (!requireNamespace("DoubletFinder", quietly = TRUE)) { # nocov start
-        stop("DoubletFinder need to be installed. Please run:\n",
-             "remotes::install_github('chris-mcginnis-ucsf/DoubletFinder')")
+        cli::cli_abort(
+            "Package {.pkg DoubletFinder} is needed for this function to work.
+            Please install it by command:
+            {.code remotes::install_github('DoubletFinder')}")
     }
     if (!requireNamespace("Seurat", quietly = TRUE)) {
-        stop("Seurat need to be installed. Please run:\n",
-             "install.packages(\"Seurat\")")
+        cli::cli_abort(
+            "Package {.pkg Seurat} is needed for this function to work.
+            Please install it by command:
+            {.code install.packages('Seurat')}")
     } # nocov end
     useDatasets <- .checkUseDatasets(object, useDatasets = useDatasets)
-    nNeighbors <- .checkArgLen(nNeighbors, length(useDatasets), repN = TRUE)
-    if (!is.null(nExp)) {
-        nExp <- .checkArgLen(nExp, length(useDatasets), repN = TRUE)
-    } else {
-        nExp <- sapply(useDatasets, function(d) {
+    nNeighbors <- .checkArgLen(nNeighbors, length(useDatasets), repN = TRUE, class = "numeric")
+    nExp <- .checkArgLen(nExp, length(useDatasets), repN = TRUE, class = "numeric")
+    if (is.null(nExp))
+        nExp <- sapply(useDatasets, function(d)
             round(0.15 * ncol(dataset(object, d)))
-        })
-    }
+        )
     object <- recordCommand(object, ...,
                             dependencies = c("Seurat", "DoubletFinder"))
     for (i in seq_along(useDatasets)) {
         d <- useDatasets[i]
-        if (isTRUE(verbose)) .log("Running DoubletFinder on dataset: ", d)
+        if (isTRUE(verbose)) cliID <- cli::cli_process_start("Running DoubletFinder on dataset {.val {d}}")
         seu <- Seurat::CreateSeuratObject(rawData(object, d)) %>%
             Seurat::NormalizeData(verbose = FALSE) %>%
             Seurat::FindVariableFeatures(verbose = FALSE) %>%
@@ -74,6 +76,7 @@ runDoubletFinder <- function(
         DFCol <- grep(pattern = "DF.classifications", colnames(seuMeta))
         cellMeta(object, "DoubletFinder_pANN", useDatasets = d) <- seuMeta[,pANNCol]
         cellMeta(object, "DoubletFinder_classification", useDatasets = d) <- seuMeta[,DFCol]
+        if (isTRUE(verbose)) cli::cli_process_done(id = cliID)
     }
     return(object)
 }

R/GSEA.R

@@ -32,22 +32,22 @@ runGSEA <- function(
         custom_gene_sets = customGenesets
 ) {
     if (!requireNamespace("org.Hs.eg.db", quietly = TRUE)) # nocov start
-        stop("Package \"org.Hs.eg.db\" needed for this function to work. ",
-             "Please install it by command:\n",
-             "BiocManager::install('org.Hs.eg.db')",
-             call. = FALSE)
+        cli::cli_abort(
+            "Package {.pkg org.Hs.eg.db} is needed for this function to work.
+            Please install it by command:
+            {.code BiocManager::install('org.Hs.eg.db')}")
 
     if (!requireNamespace("reactome.db", quietly = TRUE))
-        stop("Package \"reactome.db\" needed for this function to work. ",
-             "Please install it by command:\n",
-             "BiocManager::install('reactome.db')",
-             call. = FALSE)
+        cli::cli_abort(
+            "Package {.pkg reactome.db} is needed for this function to work.
+            Please install it by command:
+            {.code BiocManager::install('reactome.db')}")
 
     if (!requireNamespace("fgsea", quietly = TRUE))
-        stop("Package \"fgsea\" needed for this function to work. ",
-             "Please install it by command:\n",
-             "BiocManager::install('fgsea')",
-             call. = FALSE) # nocov end
+        cli::cli_abort(
+            "Package {.pkg fgsea} is needed for this function to work.
+            Please install it by command:
+            {.code BiocManager::install('fgsea')}") # nocov end
 
     .deprecateArgs(list(gene_sets = "genesets",
                         mat_w = "useW",
@@ -164,14 +164,14 @@ runGOEnrich <- function(
         ...
 ) {
     if (!requireNamespace("gprofiler2", quietly = TRUE)) # nocov start
-        stop("Package \"gprofiler2\" needed for this function to work. ",
-             "Please install it by command:\n",
-             "install.packages('gprofiler2')",
-             call. = FALSE) # nocov end
+        cli::cli_abort(
+            "Package {.pkg gprofiler2} is needed for this function to work.
+            Please install it by command:
+            {.code install.packages('gprofiler2')}") # nocov end
+
     group <- group %||% unique(result$group)
     if (any(!group %in% result$group)) {
-        stop("Selected groups not available `result$group`: ",
-             paste(group[!group %in% result$group], collapse = ", "))
+        cli::cli_abort("Selected groups not available in {.code result$group}: {.val {group[!group %in% result$group]}}")
     }
     bg <- NULL
     domain_scope <- "annotated" # gprofiler2 default
@@ -190,9 +190,9 @@ runGOEnrich <- function(
     ordered_query <- FALSE
     if (!is.null(orderBy)) {
         ordered_query <- TRUE
-        if (length(orderBy) > 1) stop("Only one `orderBy` metric allowed")
+        if (length(orderBy) > 1) cli::cli_abort("Only one {.code orderBy} metric allowed")
         if (!orderBy %in% c("logFC", "pval", "padj")) {
-            stop("`orderBy` should be one of 'logFC', 'pval' or 'padj'.")
+            cli::cli_abort("{.code orderBy} should be one of {.val logFC}, {.val pval} or {.val padj}.")
         }
         if (orderBy == "logFC") {
             resultUp <- resultUp[order(resultUp$logFC, decreasing = TRUE),]

R/classConversion.R

@@ -18,7 +18,7 @@ as.liger.dgCMatrix <- function(
     datasetVar <- droplevels(datasetVar)
 
     rawDataList <- splitRmMiss(object, datasetVar)
-    modal <- .checkArgLen(modal, length(rawDataList))
+    modal <- .checkArgLen(modal, length(rawDataList), class = "character")
     createLiger(rawData = rawDataList, modal = modal, ...)
 }
 
@@ -61,7 +61,7 @@ as.liger.SingleCellExperiment <- function(
     if (!is.factor(datasetVar)) datasetVar <- factor(datasetVar)
     datasetVar <- droplevels(datasetVar)
     raw <- splitRmMiss(raw, datasetVar)
-    modal <- .checkArgLen(modal, length(raw))
+    modal <- .checkArgLen(modal, length(raw), class = "character")
     lig <- createLiger(raw, modal = modal, ...)
     colDataCopy <- SummarizedExperiment::colData(object)
     for (cdn in colnames(colDataCopy)) {
@@ -119,7 +119,7 @@ as.liger.Seurat <- function(
     }
 
     datasetVar <- datasetVar %||% "Seurat"
-    modal <- .checkArgLen(modal, length(raw))
+    modal <- .checkArgLen(modal, length(raw), class = "character")
     lig <- createLiger(raw, modal = modal, ...)
     colnames(object) <- colnames(lig)
     for (cdn in colnames(object[[]])) {

R/classes.R

@@ -420,29 +420,28 @@ ligerSpatialDataset <- setClass(
 
 .checkCoords <- function(ld, value) {
     if (is.null(rownames(value))) {
-        warning("No rownames with given spatial coordinate, ",
-                "assuming they match with the cells.")
+        cli::cli_alert_warning("No rownames with given spatial coordinate. Assuming they match with the cells.")
         rownames(value) <- colnames(ld)
     }
     if (is.null(colnames(value))) {
         if (ncol(value) <= 3) {
             colnames(value) <- c("x", "y", "z")[seq(ncol(value))]
         } else {
-            stop("More than 3 dimensions for the coordinates but no ",
-                 "colnames are given.")
+            cli::cli_abort("More than 3 dimensions for the coordinates but no colnames are given.")
         }
-        warning("No colnames with given spatial coordinate, ",
-                "setting to ", paste0(colnames(value), collapse = ", "))
+        cli::cli_alert_warning(
+            "No colnames with given spatial coordinate. Setting to {.val {colnames(value)}}"
+        )
     }
     full <- matrix(NA, nrow = ncol(ld), ncol = ncol(value),
                    dimnames = list(colnames(ld), colnames(value)))
     cellIsec <- intersect(rownames(value), colnames(ld))
     full[cellIsec, colnames(value)] <- value[cellIsec,]
     if (any(is.na(full))) {
-        warning("NA generated for missing cells.")
+        cli::cli_alert_warning("NA generated for missing cells.")
     }
     if (any(!rownames(value) %in% rownames(full))) {
-        warning("Cells in given coordinate not found in the dataset.")
+        cli::cli_alert_warning("Cells in given coordinate not found in the dataset.")
     }
     return(full)
 }

R/clustering.R

@@ -82,7 +82,7 @@ runCluster <- function(
     if (!is.null(useDims)) H <- H[, useDims, drop = FALSE]
 
     if (isTRUE(verbose))
-        cli::cli_alert_info("{method} clustering on {type} cell factor loadings...")
+        cli::cli_process_start("{method} clustering on {type} cell factor loadings...")
     knn <- RANN::nn2(H, k = nNeighbors, eps = eps)
     snn <- ComputeSNN(knn$nn.idx, prune = prune)
     if (!is.null(seed)) set.seed(seed)
@@ -124,10 +124,10 @@ runCluster <- function(
                               verbose = verbose)
     cellMeta(object, clusterName, check = FALSE) <- clusts
     if (isTRUE(verbose))
-        cli::cli_alert_success("Found {nlevels(clusts)} clusters.")
+        cli::cli_process_done(msg_done = "{method} clustering on {type} cell factor loadings ... Found {nlevels(clusts)} clusters.")
     object@uns$defaultCluster <- object@uns$defaultCluster %||% clusterName
     if (isTRUE(verbose))
-        cli::cli_alert_info("cellMeta variable {.val {clusterName}} is now set as default.")
+        cli::cli_alert_info("cellMeta variable {.field {clusterName}} is now set as default.")
     return(object)
 }
 
@@ -291,7 +291,7 @@ mapCellMeta <- function(
     object <- recordCommand(object, ...)
     from <- cellMeta(object, from)
     if (!is.factor(from))
-        cli::cli_abort("{.code from} must be a {.cls factor}.")
+        cli::cli_abort("{.var from} must be a {.cls factor}.")
     mapping <- list(...)
     fromCats <- names(mapping)
     notFound <- fromCats[!fromCats %in% levels(from)]

R/dotplot.R

@@ -290,7 +290,10 @@ plotClusterFactorDot <- function(
     )
     if (length(viridisOption) != 1 ||
         !viridisOption %in% viridisAvail)
-        stop("`viridisOption` has to be one value from the available choices.")
+        cli::cli_abort(
+            c("{.var viridisOption} has to be one value from the available choices: ",
+              "{.val {viridisAvail}}")
+        )
 
     ## Font-size specification
     # Broadcast one-param setting to each