Close #229

openbiox · Nov 17, 2021 · 39ad478 · 39ad478
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Showing 25 changed files with 65 additions and 45 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -80,4 +80,4 @@ VignetteBuilder:
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.1.9001
+RoxygenNote: 7.1.2
diff --git a/NAMESPACE b/NAMESPACE
@@ -65,6 +65,7 @@ importFrom(psych,corr.test)
 importFrom(shiny,shinyAppFile)
 importFrom(stats,complete.cases)
 importFrom(stats,median)
+importFrom(stats,na.omit)
 importFrom(stats,prcomp)
 importFrom(stats,predict)
 importFrom(stats,quantile)

diff --git a/NEWS.md b/NEWS.md
@@ -1,5 +1,6 @@
 # UCSCXenaShiny 1.1.2
 
+- Fixed value query for gene signature with `purrr` lambda function.
 - Updated dataset doc.
 - Uploaded zenodo link.
 - Uploaded this tool to conda forge, the user can install it from conda now.

diff --git a/R/query_value.R b/R/query_value.R
@@ -107,10 +107,9 @@ query_pancan_value <- function(molecule,
     message("IDs include ", paste(ids, collapse = ", "))
     tryCatch(
       {
-        values <- lapply(ids, function(x) {
+        values <- purrr::map(ids, function(x) {
           query_value(x, data_type, database, ...)
         })
-        #values <- purrr::map(ids, ~ query_value(., data_type, database, ...))
         unit <- if (is.list(values[[1]]) && length(values[[1]]) > 1) values[[1]][[2]] else NULL
         if (is.null(unit)) {
           df <- as.data.frame(values %>% purrr::set_names(ids))

diff --git a/R/xenashiny.R b/R/xenashiny.R
@@ -5,5 +5,5 @@
 #' @import ggplot2
 #' @importFrom psych corr.test
 #' @importFrom utils download.file head install.packages tail
-#' @importFrom stats prcomp predict quantile
+#' @importFrom stats prcomp predict quantile na.omit
 NULL
diff --git a/docs/articles/api.html b/docs/articles/api.html
diff --git a/docs/articles/api_files/header-attrs-2.11/header-attrs.js b/docs/articles/api_files/header-attrs-2.11/header-attrs.js
@@ -0,0 +1,12 @@
+// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
+// be compatible with the behavior of Pandoc < 2.8).
+document.addEventListener('DOMContentLoaded', function(e) {
+  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
+  var i, h, a;
+  for (i = 0; i < hs.length; i++) {
+    h = hs[i];
+    if (!/^h[1-6]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
+    a = h.attributes;
+    while (a.length > 0) h.removeAttribute(a[0].name);
+  }
+});
diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -3,5 +3,5 @@ pkgdown: 1.6.1
 pkgdown_sha: ~
 articles:
   api: api.html
-last_built: 2021-10-05T03:28Z
+last_built: 2021-11-17T02:53Z
 
diff --git a/docs/reference/analyze_gene_drug_response_diff.html b/docs/reference/analyze_gene_drug_response_diff.html
diff --git a/docs/reference/app_run.html b/docs/reference/app_run.html
diff --git a/docs/reference/ezcor.html b/docs/reference/ezcor.html
diff --git a/docs/reference/ezcor_batch.html b/docs/reference/ezcor_batch.html
diff --git a/docs/reference/get_pancan_value.html b/docs/reference/get_pancan_value.html
diff --git a/docs/reference/load_data.html b/docs/reference/load_data.html
diff --git a/docs/reference/query_molecule_value.html b/docs/reference/query_molecule_value.html
diff --git a/docs/reference/tcga_surv_analysis.html b/docs/reference/tcga_surv_analysis.html
diff --git a/docs/reference/vis_gene_drug_response_diff.html b/docs/reference/vis_gene_drug_response_diff.html
diff --git a/docs/reference/vis_identifier_grp_comparison.html b/docs/reference/vis_identifier_grp_comparison.html