The Cell Browser allows you to group related datasets into a hierarchy, where datasets are grouped into collections, like files are grouped into directories. When you open a collection, it will show you all of the datasets within it.
This requires your datasets to be arranged in directories on disk. Let’s say
you have two directories with data files, one in directory
data1 and one in
data2, each with their own cellbrowser.conf files, then these
two directories must be both subdirectories of a parent directoryn
dataParent. The names of all the datasets
are the names of their directories, not the names
specified via the
name statement in their
cellbrowser.conf files anymore.
Specified names from cellbrowser.conf are ignored when dataset hierarchies are used
and are replaced with their directory names.
To enable dataset hierarchies, you only have to add a single line pointing to
the top-level parent directory where all of your single-cell data lives.
Add a statement like the following to your
dataRoot can be set using the
CBDATAROOT environment variable:
Then, create a “stub” cellbrowser.conf into this directory, it should only contain
a single line like
You can describe your collection as discussed under the Describing
datasets section. Put the
desc.conf file into the same directory as the
cellbrowser.conf you just created.
Define at least the statements
description. They will be
shown at the top of your dataset list. This directory can be called the
Arrange your dataset directories under this directory. You can add empty directories,
which will become collections, by creating dataset directories in them and put a
desc.conf into it, e.g. like this:
mkdir -p /celldata/organoids cd /celldata/organoids echo 'name="organoids"' > cellbrowser.conf echo 'shortLabel="Brain Organoids"' >> cellbrowser.conf echo 'tags=["10x"]' >> cellbrowser.conf
Now you can run
cbBuild in each subdirectory of a collection.
in the collection. Or you can rebuild in all subdirectories using
If you view the cell browser now using a web browser, you should see this new collection present. When viewing a dataset in a collection, you can move quickly to any other dataset in the same collection using the “Collection” dropdown menu in the toolbar.