Merge branch 'develop' into seurat5

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: Signac
 Title: Analysis of Single-Cell Chromatin Data
-Version: 1.11.9000
-Date: 2023-09-20
+Version: 1.12.9000
+Date: 2023-10-13
 Authors@R: c(
   person(given = 'Tim', family = 'Stuart', email = '[email protected]', role = c('aut', 'cre'), comment = c(ORCID = '0000-0002-3044-0897')),
   person(given = 'Avi', family = 'Srivastava', email = '[email protected]', role = 'aut', comment = c(ORCID = '0000-0001-9798-2079')),

NEWS.md

@@ -1,4 +1,4 @@
-# Unreleased
+# Signac 1.11.0
 
 Bug fixes:
 

vignettes/data_structures.Rmd

@@ -483,6 +483,17 @@ packages. Position frequency matrices for motifs can be loaded using the
 or the [chromVARmotifs](https://github.com/GreenleafLab/chromVARmotifs) package.
 For example:
 
+```{r include=FALSE}
+if (!requireNamespace("JASPAR2020", quietly = TRUE))
+    BiocManager::install("JASPAR2020")
+if (!requireNamespace("TFBSTools", quietly = TRUE))
+    BiocManager::install("TFBSTools")
+if (!requireNamespace("motifmatchr", quietly = TRUE))
+    BiocManager::install("motifmatchr")
+if (!requireNamespace("BSgenome.Hsapiens.UCSC.hg19", quietly = TRUE))
+    BiocManager::install("BSgenome.Hsapiens.UCSC.hg19")
+```
+
 ```{r message=FALSE, warning=FALSE}
 library(JASPAR2020)
 library(TFBSTools)

vignettes/pbmc_multiomic.Rmd

@@ -133,14 +133,26 @@ peaks <- CallPeaks(pbmc)
 # remove peaks on nonstandard chromosomes and in genomic blacklist regions
 peaks <- keepStandardChromosomes(peaks, pruning.mode = "coarse")
 peaks <- subsetByOverlaps(x = peaks, ranges = blacklist_hg38_unified, invert = TRUE)
+```
 
+```{r include=FALSE}
+gc()
+```
+
+```{r message=FALSE, warning=FALSE}
 # quantify counts in each peak
 macs2_counts <- FeatureMatrix(
   fragments = Fragments(pbmc),
   features = peaks,
   cells = colnames(pbmc)
 )
+```
 
+```{r include=FALSE}
+gc()
+```
+
+```{r}
 # create a new assay using the MACS2 peak set and add it to the Seurat object
 pbmc[["peaks"]] <- CreateChromatinAssay(
   counts = macs2_counts,
@@ -189,7 +201,7 @@ Installation instructions for SeuratDisk can be found [here](https://github.com/
 library(SeuratDisk)
 
 # load PBMC reference
-reference <- LoadH5Seurat("../vignette_data/multiomic/pbmc_multimodal.h5seurat")
+reference <- LoadH5Seurat("../vignette_data/multiomic/pbmc_multimodal.h5seurat", assays = list("SCT" = "counts"), reductions = 'spca')
 reference <- UpdateSeuratObject(reference)
 
 DefaultAssay(pbmc) <- "SCT"