Reformat with air

Author: jayhesselberth

.Rbuildignore

@@ -12,3 +12,5 @@
 ^inst/manuscript$
 ^\.github$
 ^CODE_OF_CONDUCT\.md$
+^air.toml$
+^\.vscode$

.vscode/settings.json

@@ -0,0 +1,6 @@
+{
+    "[r]": {
+        "editor.formatOnSave": true,
+        "editor.defaultFormatter": "Posit.air-vscode"
+    }
+}

R/cellbrowsers.R

@@ -26,67 +26,66 @@
 #' )
 #' }
 #' @export
-get_ucsc_reference <- function(cb_url,
-                               cluster_col,
-                               ...) {
-    if (!requireNamespace("R.utils", quietly = TRUE)) {
-        stop(
-            "This function requires the R.utils package, please install\n",
-            "install.packages('R.utils')"
-        )
-    }
+get_ucsc_reference <- function(cb_url, cluster_col, ...) {
+  if (!requireNamespace("R.utils", quietly = TRUE)) {
+    stop(
+      "This function requires the R.utils package, please install\n",
+      "install.packages('R.utils')"
+    )
+  }
 
-    if (!requireNamespace("data.table", quietly = TRUE)) {
-        stop(
-            "This function requires the data.table package, please install\n",
-            "install.packages('data.table')"
-        )
-    }
+  if (!requireNamespace("data.table", quietly = TRUE)) {
+    stop(
+      "This function requires the data.table package, please install\n",
+      "install.packages('data.table')"
+    )
+  }
 
-    url <- httr::parse_url(cb_url)
-    base_url <- url
-    ds <- url$query$ds
+  url <- httr::parse_url(cb_url)
+  base_url <- url
+  ds <- url$query$ds
 
-    # ds can include sub-datasets with syntax, "dataset+subdataset+and-so-on"
-    # files are hosted at urls: dataset/subdataset/andsoon/..."
-    ds_split <- strsplit(ds, "+", fixed = TRUE)[[1]]
-    ds <- paste0(ds_split, collapse = "/")
-    base_url$query <- ""
+  # ds can include sub-datasets with syntax, "dataset+subdataset+and-so-on"
+  # files are hosted at urls: dataset/subdataset/andsoon/..."
+  ds_split <- strsplit(ds, "+", fixed = TRUE)[[1]]
+  ds <- paste0(ds_split, collapse = "/")
+  base_url$query <- ""
 
-    mdata_url <- httr::modify_url(base_url,
-        path = file.path(ds, "meta.tsv")
-    )
-    if (!httr::http_error(mdata_url)) {
-        mdata <- data.table::fread(mdata_url, data.table = FALSE, sep = "\t")
-    } else {
-        stop("unable to find metadata at url: ", mdata_url)
-    }
+  mdata_url <- httr::modify_url(base_url, path = file.path(ds, "meta.tsv"))
+  if (!httr::http_error(mdata_url)) {
+    mdata <- data.table::fread(mdata_url, data.table = FALSE, sep = "\t")
+  } else {
+    stop("unable to find metadata at url: ", mdata_url)
+  }
 
-    mat_url <- httr::modify_url(base_url,
-        path = file.path(ds, "exprMatrix.tsv.gz")
-    )
-    if (!httr::http_error(mat_url)) {
-        mat <- data.table::fread(mat_url, data.table = FALSE, sep = "\t")
-    } else {
-        stop("unable to find matrix at url: ", mat_url)
-    }
+  mat_url <- httr::modify_url(
+    base_url,
+    path = file.path(ds, "exprMatrix.tsv.gz")
+  )
+  if (!httr::http_error(mat_url)) {
+    mat <- data.table::fread(mat_url, data.table = FALSE, sep = "\t")
+  } else {
+    stop("unable to find matrix at url: ", mat_url)
+  }
 
-    rownames(mat) <- mat[, 1]
-    mat[, 1] <- NULL
-    mat <- as.matrix(mat)
+  rownames(mat) <- mat[, 1]
+  mat[, 1] <- NULL
+  mat <- as.matrix(mat)
 
-    mm <- max(mat)
+  mm <- max(mat)
 
-    if (mm > 50) {
-        dots <- list(...)
-        if (!"if_log" %in% names(dots) || dots$if_log) {
-            warning(
-                "the data matrix has a maximum value of ", mm, "\n",
-                "the data are likely not log transformed,\n",
-                "please set the if_log argument for average clusters accordingly"
-            )
-        }
+  if (mm > 50) {
+    dots <- list(...)
+    if (!"if_log" %in% names(dots) || dots$if_log) {
+      warning(
+        "the data matrix has a maximum value of ",
+        mm,
+        "\n",
+        "the data are likely not log transformed,\n",
+        "please set the if_log argument for average clusters accordingly"
+      )
     }
+  }
 
-    average_clusters(mat, mdata, cluster_col = cluster_col, ...)
+  average_clusters(mat, mdata, cluster_col = cluster_col, ...)
 }