Is your feature request related to a problem? Please describe.
When I create a data analysis script, I ofter include code to draw the basic manual gates that I need to run with new data set. If I am rerunning the script, of course, these gate are already in the gating template, so I often include a cyto_gatingTemplate_apply(gsSamp, "Samples-Template.csv") at the end of the gate series. The latter is smart enough to ignore gates I've just created manually if it is the firs run. However, if I attempt to recreate a manual gate that is in the template I get an error. This seems to mean I can not run the whole script if the template already exists because this error halts the script.
> # Gate (non-debris) Cells (Samples-Template.csv)
> cyto_gate_draw(gsSamp,
+ parent = "root",
+ alias = "Non-Debris",
+ channels = c("FSC-AREA", "SSC-AREA"))
Non-Debris already exists in Samples-Template.csv.
Error in FUN(X[[i]], ...) :
Supply another gatingTemplate or edit gate(s) using cyto_gate_edit.
Describe the solution you'd like
I'm not certain whether it would be possible to turn this into a warning instead of an error, so that I could run the script from beginning to end without it stopping on these gate creation lines, or alternatively have a flag that would ignore a cyto_gate_draw() request if it were already in the template. I could manually implement an ifexists solution in my own script, but I would need a way to test existence, and I don't currently know how to do that.
This is not a big deal but I commonly find myself re-running a script on each of the experiments in a protocol set after changing my mind about the graphs or staticial approach to data analysis. I have to babysit each run even after completing the new cyto_setup shiny clicks.
Perhaps there are reasons this makes no sense, and I continue to appreciate this fine package.
Is your feature request related to a problem? Please describe. When I create a data analysis script, I ofter include code to draw the basic manual gates that I need to run with new data set. If I am rerunning the script, of course, these gate are already in the gating template, so I often include a cyto_gatingTemplate_apply(gsSamp, "Samples-Template.csv") at the end of the gate series. The latter is smart enough to ignore gates I've just created manually if it is the firs run. However, if I attempt to recreate a manual gate that is in the template I get an error. This seems to mean I can not run the whole script if the template already exists because this error halts the script.
Describe the solution you'd like I'm not certain whether it would be possible to turn this into a warning instead of an error, so that I could run the script from beginning to end without it stopping on these gate creation lines, or alternatively have a flag that would ignore a cyto_gate_draw() request if it were already in the template. I could manually implement an ifexists solution in my own script, but I would need a way to test existence, and I don't currently know how to do that.
This is not a big deal but I commonly find myself re-running a script on each of the experiments in a protocol set after changing my mind about the graphs or staticial approach to data analysis. I have to babysit each run even after completing the new cyto_setup shiny clicks.
Perhaps there are reasons this makes no sense, and I continue to appreciate this fine package.