Hi Guys,

Here are some questions.

1. Is this possible to examine a FlowJo workspace in openCyto only in order to convert it into a gating template?
2. It is possible to create a combination of gates ie. ifn+/-il2+/-il4+/-il10+/-tnf+/- ? I am trying with refGate-mindensity but it didn't work. Does exists a similar function as "boolean gates" found in FlowJo. When I use refGate-mindensity I am having the following error:

   "expanding pop: cd4-/+cd8+/-

   Error in .preprocess_row(this_row) :
     ifn+/-il2+/-il4+/-il10+/-tnf+/- has invalid number of dimensions: 5"

3. I am also trying to create new gates with alias-created populations like: ifn+ producing cells from a population CD45RO+CD197+ but it also did not work. I received the following error:

"expanding pop: cd4-/+cd8+/-

expanding pop: cd45ro+/-cd197+/-

expanding pop: cd45ro+/-cd197+/-

Error in .getFullPath(this_row[, parent], new_dt) :
  Non-unique reference to: cd45ro+cd197+"

Using from malaria_gate .csv (link at the end)

> dtTemplate[17,]
      alias      pop        parent    dims gating_method       gating_args collapseDataForGating groupBy preprocessing_method preprocessing_args
1: tcm_ifng tcm_ifng cd45ro+cd197+ fsa,ifn    mindensity gate_range=c(1,3)                    NA      NA                                      NA

I am also sending attached two .csv file with two possible gating structures.

The first one I created worked (https://www.dropbox.com/s/8n21icd4cvps7w4/gate_malaria.csv?dl=0) but I am stuck when trying to apply more complex gates, like in (https://www.dropbox.com/s/cubzfbqq9oan9wm/large_malaria.csv?dl=0) because I think I am being redundant with the populations, and because I couldn't create the combination of gates.

Thanks a lot for any advice or suggestion that you can give me.

Bests

1. try 'help(templateGen)'

2. set 'method' to 'boolGate' and 'args' to 'ifn+&il2+&...' (use '|' for 'or' operations)

I'd add

1. Use `templateGen`, but you'll need to parse at least one sample to generate a GatingSet. Write the output to file and fill in the missing details. The generated template is just a skeleton.

2. The `polyFunctions` gate may be what you are looking for, as it will generate all boolean combinations of the inputs. It is there for convenience when there are many markers. Pass the markers to the `gating_args` column in the template. I think the documentation is a bit sparse at the moment on the specific syntax. We'll address that. 

3. Not certain, but you may need to ensure you refer to gates by unique gating paths. In this case, the gate can likely refer to a gate parented by CD4 or CD8.