added badges

R/functions.R

@@ -379,11 +379,12 @@ plot.cornet <- function(x,...){
   
   # colours
   if("RColorBrewer" %in% .packages(all.available=TRUE)){
-    pal <- rev(c("white",RColorBrewer::brewer.pal(n=9,name="Blues")))
+    pal <- rev(c("white",RColorBrewer::brewer.pal(n=9,name="Greys")))
     col <- grDevices::colorRampPalette(colors=pal)(k)
   } else {
     col <- grDevices::heat.colors(n=k)
   }
+  #col <- grDevices::grey(level=seq(from=0,to=1,length.out=k))
   
   nsigma <- length(x$sigma)
   npi <- length(x$pi)

docs/articles/vignette.html

@@ -114,7 +114,7 @@
 <p>We use the Bioconductor packages <a href="https://doi.org/10.18129/B9.bioc.GEOquery"><code>GEOquery</code></a> and <a href="https://doi.org/10.18129/B9.bioc.Biobase"><code>Biobase</code></a> for obtaining the data <span class="math inline">\((\approx 150\)</span>MB<span class="math inline">\()\)</span>:</p>
 <div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1"><span class="co">#install.packages("BiocManager")</span></a>
 <a class="sourceLine" id="cb4-2" title="2"><span class="co">#BiocManager::install(c("GEOquery","Biobase"))</span></a>
-<a class="sourceLine" id="cb4-3" title="3">data &lt;-<span class="st"> </span>GEOquery<span class="op">::</span><span class="kw">getGEO</span>(<span class="dt">GEO=</span><span class="st">"GSE80599"</span>)[[<span class="dv">1</span>]]</a>
+<a class="sourceLine" id="cb4-3" title="3">data &lt;-<span class="st"> </span>GEOquery<span class="op">::</span><span class="kw"><a href="https://rdrr.io/pkg/GEOquery/man/getGEO.html">getGEO</a></span>(<span class="dt">GEO=</span><span class="st">"GSE80599"</span>)[[<span class="dv">1</span>]]</a>
 <a class="sourceLine" id="cb4-4" title="4">pheno &lt;-<span class="st"> </span>Biobase<span class="op">::</span><span class="kw"><a href="https://rdrr.io/pkg/Biobase/man/phenoData.html">pData</a></span>(data)</a>
 <a class="sourceLine" id="cb4-5" title="5">y &lt;-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/numeric.html">as.numeric</a></span>(pheno<span class="op">$</span><span class="st">`</span><span class="dt">updrs-mds3.12 score:ch1</span><span class="st">`</span>)</a>
 <a class="sourceLine" id="cb4-6" title="6">age &lt;-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/numeric.html">as.numeric</a></span>(pheno<span class="op">$</span><span class="st">`</span><span class="dt">age at examination (years):ch1</span><span class="st">`</span>)</a>