fixed a bug in getTopFeatures()

jyyulab · Nov 13, 2024 · a2d02bc · a2d02bc
1 parent 07ffa04
commit a2d02bc
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Showing 64 changed files with 501 additions and 261 deletions.
diff --git a/R/differential_analysis.R b/R/differential_analysis.R
@@ -448,7 +448,7 @@ getTopFeatures <- function(input_table,
   for (i in 1:length(grps)) {
     table.sel <- input_table.sorted[input_table.sorted[, group_by] %in% c(grps[i]), , drop = FALSE]
     if (nrow(table.sel) >= number) {
-      if (i == 1) {table_res <- table.sel[c(1:number),]} else {table_res <- rbind(table_res, table.sel[number,])}
+      if (i == 1) {table_res <- table.sel[c(1:number),]} else {table_res <- rbind(table_res, table.sel[c(1:number),])}
     } else {
       if (i == 1) {table_res <- table.sel} else {table_res <- rbind(table_res, table.sel)}
     }

diff --git a/R/network_analysis.R b/R/network_analysis.R
@@ -396,15 +396,12 @@ generateSJARACNeInput <- function(input_eset,
 #'
 #' @examples
 #' \dontrun{
-#' ## 1. assess the quality of network from network files
-#' drawNetworkQC(network_file = /project_space/SJARACNE/B/SIG/b100/consensus_network_ncol_.txt, generate_html = TRUE)
-#' drawNetworkQC(network_file = /project_space/SJARACNE/B/SIG/b100/consensus_network_ncol_.txt, generate_html = TRUE,
-#'               outdir = "/path-to-cutomized-folder")
-#' drawNetworkQC(network_file = /project_space/SJARACNE/B/SIG/b100/consensus_network_ncol_.txt, generate_html = TRUE,
-#'               prefix = "PBMC14")
+#' ## 1. Assess the quality of network from network files
+#' drawNetworkQC(network_file = "/project_space/SJARACNE/B/SIG/b100/consensus_network_ncol_.txt", generate_html = TRUE,
+#'               outdir = "/folder-to-save-report_file", prefix = "PBMC14")
 #'
-#' ## 2. assess the quality of network from the directory of network files
-#' drawNetworkQC(sjaracne_dir = /project_space/SJARACNE, generate_html = TRUE)
+#' ## 2. Assess the quality of network from the directory of network files
+#' drawNetworkQC(sjaracne_dir = "/project_space/SJARACNE", generate_html = TRUE)
 #' }
 #'
 drawNetworkQC <- function(network_file = NULL,

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/LICENSE.html b/docs/LICENSE.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/articles/quick_tutorial.html b/docs/articles/quick_tutorial.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/pkgdown.js b/docs/pkgdown.js
@@ -152,3 +152,11 @@ async function searchFuse(query, callback) {
   });
   });
 })(window.jQuery || window.$)
+
+document.addEventListener('keydown', function(event) {
+  // Check if the pressed key is '/'
+  if (event.key === '/') {
+    event.preventDefault();  // Prevent any default action associated with the '/' key
+    document.getElementById('search-input').focus();  // Set focus to the search input
+  }
+});
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -1,9 +1,9 @@
 pandoc: 3.1.11
-pkgdown: 2.1.0
+pkgdown: 2.1.1
 pkgdown_sha: ~
 articles:
   quick_tutorial: quick_tutorial.html
-last_built: 2024-09-20T19:02Z
+last_built: 2024-11-13T18:54Z
 urls:
   reference: https://jyyulab.github.io/scMINER/reference
   article: https://jyyulab.github.io/scMINER/articles
diff --git a/docs/reference/MICAplot.html b/docs/reference/MICAplot.html
diff --git a/docs/reference/SparseExpressionSet-class.html b/docs/reference/SparseExpressionSet-class.html
diff --git a/docs/reference/addMICAoutput.html b/docs/reference/addMICAoutput.html
diff --git a/docs/reference/cal_Activity.html b/docs/reference/cal_Activity.html
diff --git a/docs/reference/combinePvalVector.html b/docs/reference/combinePvalVector.html