fix a bug that missing sqrt in the mds function

DavisLaboratory · Oct 24, 2023 · bc7ce67 · bc7ce67
1 parent 62dff22
commit bc7ce67
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/.DS_Store b/.DS_Store
diff --git a/R/plotDR.R b/R/plotDR.R
@@ -329,8 +329,8 @@ pdataMDS_intl <- function(mdsdata, dims) {
   lambda <- pmax(mdsdata$eigen.values, 0)
   plotdf <- data.frame(
     "RestoolsMtchID" = rownames(mdsdata$distance.matrix.squared),
-    x = mdsdata$eigen.vectors[, dims[1]] * lambda[dims[1]],
-    y = mdsdata$eigen.vectors[, dims[2]] * lambda[dims[2]]
+    x = mdsdata$eigen.vectors[, dims[1]] * sqrt(lambda[dims[1]]),
+    y = mdsdata$eigen.vectors[, dims[2]] * sqrt(lambda[dims[2]])
   )
   pca_labs <- paste0("Leading logFC dim ", seq(ncol(mdsdata$eigen.vectors)))
   pca_labs <- paste0(pca_labs, " (", round(mdsdata$var.explained * 100, digits = 2), "%)")