update vignette

shahcompbio · Oct 1, 2024 · cde8ca4 · cde8ca4
1 parent 92aadaf
commit cde8ca4
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Showing 2 changed files with 6 additions and 6 deletions.
diff --git a/R/callHSCN.R b/R/callHSCN.R
@@ -724,13 +724,13 @@ callHaplotypeSpecificCN <- function(CNbins,
 
   if (female == TRUE){
     #do not infer states for chr "Y"
-    haplotypes <- dplyr::filter(haplotypes, chr != "Y")
-    CNbins <- dplyr::filter(CNbins, chr != "Y")
+    #haplotypes <- dplyr::filter(haplotypes, chr != "Y")
+    #CNbins <- dplyr::filter(CNbins, chr != "Y")
   } else{
     #do not infer states for chr "X" or "Y"
-    haplotypes <- dplyr::filter(haplotypes, chr != "Y")
+    #haplotypes <- dplyr::filter(haplotypes, chr != "Y")
     haplotypes <- dplyr::filter(haplotypes, chr != "X")
-    CNbins <- dplyr::filter(CNbins, chr != "Y")
+    #CNbins <- dplyr::filter(CNbins, chr != "Y")
   }
 
   nhaplotypes <- haplotypes %>% 

diff --git a/vignettes/ASCN.Rmd b/vignettes/ASCN.Rmd
@@ -97,9 +97,9 @@ There are also some function to plot per cell BAF and state plots. You can speci
 plotCNprofileBAF(hscn, cellid = "SA921-A90554A-R03-C44")
 ```
 
-Here we'll plot an equivalent plot merging data across cell clusters using the utility function `consensyscopynumber`. Here, the `cell_id` column becomes the 
-```{r, fig.show='hold', fig.height=5 , fig.width=10}
+Here we'll plot an equivalent plot merging data across cell clusters using the utility function `consensyscopynumber`. Here, the `cell_id` column becomes the `clone_id`.
 
+```{r, fig.show='hold', fig.height=5 , fig.width=10}
 consensus_clusters <- consensuscopynumber(hscn$data, cl = cl$clustering)
 
 plotCNprofileBAF(consensus_clusters, cellid = "A")