| When you drag a node onto another
sample, then FlowJo checks to see if the destination node
already has a gate with the name of the node that you are
dragging.
Thus, if you are dragging a Lymphocyte gate onto a sample
which already has a lymphocyte gate, your options are
three-fold. These options are presented to you via the node replacement
dialog window.
(1) You may choose to Replace the existing
gate with the version that you are dragging. Do this when
you want to make the destination sample's gate the same as
the one you are dragging.
(2) You may choose to Duplicate the
existing gate. It will be added to the sample, but it's
name will be modified by appending a version number to the
name (for instance, the new gate will be named
"Lymphocyte-2" in this example).
(3) You may choose to Retain the gate in
the destination sample. Initially, this option may sound
like it is useless, but in fact it is one of the most
important features of FlowJo, so it is important to
recognize how it works. With this option, FlowJo will not
alter any of the gates in the destination sample; their
specific versions of any particular gate will remain as
they are.
If you are dragging only a single population, then the Retain
option causes nothing to happen; i.e., it is not useful for
this case.
But consider the case where you are dragging a whole
tree of analyses: now you can use this option to add only
the specific analyses or gates that the destination doesn't
have, without changing the gates that already existed in
the destination (because they may be slightly different
than they are in the source sample). For example, let's
assume that you have gated two samples for lymphocytes, but
the gates are slightly different. You gave the gates the
same name in each sample (Lymphocytes), because they
identify the same subset of cells. In the first sample, you
then generate additional gates to identify subsets of
lymphocytes, like CD4 and CD8 T cells.
By clicking on the first sample's lymphocyte population
while holding down the option key, you
will drag the entire tree (all of the subsets below
lymphocytes); this is how you duplicate all analyses
quickly across samples. When you drag this whole tree to
the second sample, you want only the new analyses to be
added in the appropriate locations (i.e., the CD4 and CD8
gates to be attached to the existing lymphocyte gate). Here
is where you would choose the "retain" option: now as
FlowJo adds the dragged tree onto the sample, it will
retain all of the old gates that have the same name
(Lymphocytes). It then adds the CD4 and CD8 gates to this
gate.
If you had chosen the Replace option, then
the lymphocyte gate itself would have been changed to be
identical to first one, and then the remaining nodes (CD4
and CD8 gates) would be added to it. Choose this option if
you want all of the analyses and gates in both the source
and the destination to be identical.
Again, the Retain option allows you to
copy analyses (and populations) without changing any
specific changes you made for a specific sample.
One final note: when you drag nodes to a group, then you
are not presented with the dialog giving you the options.
Rather, FlowJo assumes that you wish to Replace
the versions of the group nodes with the ones you are
dragging. This means that all samples which have the
group's version of the nodes you are dragging will have
their nodes updated as well. For more information, see the
pages on Groups.
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