Diff of /R/XenaBrowse.R [000000] .. [0bdad5]

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+#' View Info of Dataset or Cohort at UCSC Xena Website Using Web browser
+#'
+#' This will open dataset/cohort link of UCSC Xena
+#' in user's default browser.
+#' @param x a [XenaHub] object.
+#' @param type one of "dataset" and "cohort".
+#' @param multiple if `TRUE`, browse multiple links instead of throwing error.
+#' @importFrom utils URLencode browseURL
+#' @export
+#'
+#' @examples
+#' \donttest{
+#' XenaGenerate(subset = XenaHostNames == "tcgaHub") %>%
+#'   XenaFilter(filterDatasets = "clinical") %>%
+#'   XenaFilter(filterDatasets = "LUAD") -> to_browse
+#' }
+XenaBrowse <- function(x, type = c("dataset", "cohort"), multiple = FALSE) { # nocov start
+  if (!inherits(x, "XenaHub")) {
+    stop("Input x must be a XenaHub object.")
+  }
+
+  type <- match.arg(type)
+
+  if (type == "dataset") {
+    all_datasets <- datasets(x)
+    if (length(all_datasets) != 1) {
+      if (!multiple) stop("This function limite 1 dataset to browse.\n Set multiple to TRUE if you want to browse multiple links.")
+      for (i in all_datasets) {
+        xe_tmp <- XenaFilter(x,
+          filterDatasets = i,
+          ignore.case = FALSE, fixed = TRUE
+        )
+        y <- utils::URLencode(
+          paste0(
+            "https://xenabrowser.net/datapages/?",
+            "dataset=", datasets(xe_tmp),
+            "&host=", hosts(xe_tmp)
+          )
+        )
+        utils::browseURL(y)
+      }
+    } else {
+      y <- utils::URLencode(
+        paste0(
+          "https://xenabrowser.net/datapages/?",
+          "dataset=", datasets(x),
+          "&host=", hosts(x)
+        )
+      )
+      utils::browseURL(y)
+    }
+  } else {
+    all_cohorts <- cohorts(x)
+    if (length(all_cohorts) != 1) {
+      if (!multiple) stop("This function limite 1 cohort to browse. \n Set multiple to TRUE if you want to browse multiple links.")
+      for (i in all_cohorts) {
+        xe_tmp <- XenaFilter(x,
+          filterCohorts = i,
+          ignore.case = FALSE, fixed = TRUE
+        )
+        y <- utils::URLencode(
+          paste0(
+            "https://xenabrowser.net/datapages/?",
+            "cohort=", cohorts(xe_tmp)
+          )
+        )
+        utils::browseURL(y)
+      }
+    } else {
+      y <- utils::URLencode(
+        paste0(
+          "https://xenabrowser.net/datapages/?",
+          "cohort=", cohorts(x)
+        )
+      )
+      utils::browseURL(y)
+    }
+  }
+
+  invisible(NULL)
+} # nocov end
+
+utils::globalVariables(c("XenaDatasets", "XenaHosts", "ProbeMap"))