Describe the bugcyto_plot_gating_tree does not function on GatingTemplates where pop "*" is used to generate multiple aliases from one line. During preprocessing, dummy gates are created within the template object (presumably for internal use).
In cyto_plot_gating_tree.GatingTemplate, the template is converted into a data.table. That table has duplicate aliases due to the dummy gates and fails when calling CytoExploreR_.preprocess_csv.
To Reproduce
Steps to reproduce the behavior:
Create a GatingTemplate csv containing a row that uses quad_gate_sequential with a list of aliases and pop = "*"
Eg. alias = "A,B,C,D", pop = "*"
Create a GatingTemplate object using gatingTemplate(path)
Call cyto_plot_gating_tree on the GatingTemplate object
Expected behavior
A plot in the standard form of cyto_plot_gating_tree should be generated with the quad gate represented by the parent node splitting into four separate nodes.
Screenshots
Error message from preprocess_csv. 'A' is the alias name. Missing space is an error in openCyto.
Desktop (please complete the following information):
Describe the bug
cyto_plot_gating_treedoes not function on GatingTemplates where pop "*" is used to generate multiple aliases from one line. During preprocessing, dummy gates are created within the template object (presumably for internal use).In
cyto_plot_gating_tree.GatingTemplate, the template is converted into a data.table. That table has duplicate aliases due to the dummy gates and fails when callingCytoExploreR_.preprocess_csv.To Reproduce Steps to reproduce the behavior:
gatingTemplate(path)cyto_plot_gating_treeon theGatingTemplateobjectExpected behavior A plot in the standard form of
cyto_plot_gating_treeshould be generated with the quad gate represented by the parent node splitting into four separate nodes.Screenshots
Error message from preprocess_csv. 'A' is the alias name. Missing space is an error in openCyto.
Desktop (please complete the following information):