add scale to degSignature

NEWS

@@ -1,7 +1,8 @@
 DEGreport News
 
 CHANGES IN DEGreport 1.21.2
-
+
+    * Feature: add `scale` option to degSignature
     * Feature: add lfdr support from fdrtools to degCombs and DEGSet object.
 
 CHANGES IN DEGreport 1.21.1

R/clustering.R

@@ -71,6 +71,7 @@
 #' degPlotCluster(table, "group", "other", process = TRUE)
 #' @export
 degPlotCluster <- function(table, time, color = NULL,
+                           min_genes = 10,
                            process = FALSE,
                            points = TRUE,
                            boxes = TRUE,
@@ -89,6 +90,7 @@ degPlotCluster <- function(table, time, color = NULL,
 
     if ("cluster"  %in% colnames(table)){
         counts <- table(distinct(table, genes, cluster)[["cluster"]])
+        counts <- counts[counts>=min_genes]
         table <- inner_join(table,
                             data.frame(cluster = as.integer(names(counts)),
                                        title = paste(names(counts),

R/signature.R

@@ -36,14 +36,19 @@
 #'   should match \code{ma} column names
 #'   row number should be the same length than p-values vector.
 #' @param slot slotName in the case of SummarizedExperiment objects.
+#' @param scale Whether to scale or not the expression.
 #' @return ggplot plot.
 #' @examples
 #' data(humanGender)
 #' data(geneInfo)
 #' degSignature(humanGender, geneInfo, group = "group")
 #' @export
-degSignature <- function(counts, signature, group = NULL, metadata = NULL, slot = 1){
+degSignature <- function(counts, signature,
+                         group = NULL, metadata = NULL,
+                         slot = 1, scale = FALSE){
     c <- .get_counts(counts, slot)
+    if (scale)
+        c <- t(scale(t(c)))
     meta <- .get_meta(counts)
     if (is.null(meta))
         meta <- metadata

_pkgdown.yml

@@ -1,23 +1,63 @@
-url: http://lpantano.github.io/DEGreport
+reference:
+- title: All functions
+  desc: null
+  contents:
+  - '`DEGSet`'
+  - '`DEGreport-package`'
+  - '`createReport`'
+  - '`deg`'
+  - '`degCheckFactors`'
+  - '`degColors`'
+  - '`degComps`'
+  - '`degCorCov`'
+  - '`degCovariates`'
+  - '`degDefault`'
+  - '`degFilter`'
+  - '`degMA`'
+  - '`degMB`'
+  - '`degMDS`'
+  - '`degMV`'
+  - '`degMean`'
+  - '`degMerge`'
+  - '`degObj`'
+  - '`degPCA`'
+  - '`degPatterns`'
+  - '`degPlot`'
+  - '`degPlotCluster`'
+  - '`degPlotWide`'
+  - '`degQC`'
+  - '`degResults`'
+  - '`degSignature`'
+  - '`degSummary`'
+  - '`degVB`'
+  - '`degVar`'
+  - '`degVolcano`'
+  - '`geneInfo`'
+  - '`geom_cor`'
+  - '`humanGender`'
+  - '`significants`'
+articles:
+- title: All vignettes
+  desc: null
+  contents: '`DEGreport`'
+navbar:
+  structure:
+    left:
+    - home
+    - intro
+    - reference
+    - articles
+    - tutorials
+    - news
+    right: github
+  components:
+    home:
+      icon: fa-home fa-lg
+      href: index.html
+    reference:
+      text: Reference
+      href: reference/index.html
+    intro:
+      text: Get started
+      href: articles/DEGreport.html
 
-template:
-  params:
-    bootswatch: readable
-
-authors:
-    Lorena Pantano:
-        href: https://lpantano.github.io
-    Michael Steinbaugh:
-        href: http://steinbaugh.com
-    Rory Kirchner:
-        href: https://github.com/roryk
-    Victor Barrera:
-        href: https://github.com/vbarrera
-    Kenneth Daily:
-    Thanneer Malai Perumal:
-    Mary Piper:
-        href: https://github.com/marypiper
-    John Hutchinson:
-        href: https://github.com/jnhutchinson
-    Harvard Chan Bioinformatics Core:
-        href: http://bioinformatics.sph.harvard.edu