Add requirements (HDF5 version 1.10.1 at least is needed) to README.m…

…d. Update tutorial (removed dgem argument from add_scenic_regulons).

README.md

@@ -2,6 +2,19 @@
 An R package (compatible with SCope) to create generic .loom files and extend them with other data e.g.: SCENIC regulons, Seurat clusters and markers, ... The package can also be used to extract
 data from .loom files.
 
+## Requirements
+- HDF5 >= 1.10.1
+
+Version 1.10.1 can be installed with this snippet:
+```
+wget https://support.hdfgroup.org/ftp/HDF5/current/src/hdf5-1.10.1.tar
+cd hdf5-1.10.1
+./configure
+make -j4
+make check
+make install
+```
+
 ## Installation
 
 Installation should take less than one minute.

vignettes/SCopeLoomR_tutorial.Rmd

@@ -99,7 +99,6 @@ add_col_attr(loom=loom, key = "Cell type", value=cell.info$cellType, as.annotati
 add_col_attr(loom=loom, key = "nGene", value=cell.info$nGene, as.metric = T)
 ```
 
-
 ## Add SCENIC results (Optional)
 
 *(Not run in this example)*
@@ -117,7 +116,6 @@ add_scenic_regulons_auc_matrix(loom=loom, regulons.AUC=getAUC(regulons.AUC))
 load(paste0(scenic.dir, "int/3.0_regulons_forAUCell.RData"), verbose=TRUE)
 regulon.enrichment.table<-read.table(file = "output/Step2_MotifEnrichment.tsv", header = T, sep = "\t", quote = '', stringsAsFactors = F)
 add_scenic_regulons(loom=loom
-                    , dgem=dgem
                     , regulons=regulons
                     , regulon.threshold.assignments=...$threshold.assignment # Optional
                     , regulon.enrichment.table = regulon.enrichment.table # Optional) 
@@ -216,7 +214,7 @@ dgem<-get_dgem(loom = loom)
 
 ```{r}
 loom<-open_loom(loom = "Aerts_Fly_AdultBrain_Filtered_57k.loom")
-cluster.10.dgem<-get_cluster_dgem_by_name(loom = loom, cluster.name = "MBON - Cluster 57")
+cluster.10.dgem<-get_cluster_dgem_by_name(loom = loom, cluster.name = "Astrocyte-like - Cluster 10")
 ```