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cyto_plot_gating_tree does not support pop "*" in GatingTemplate #186

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RSM151 opened this issue Jun 21, 2023 · 0 comments
Open

cyto_plot_gating_tree does not support pop "*" in GatingTemplate #186

RSM151 opened this issue Jun 21, 2023 · 0 comments
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@RSM151
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RSM151 commented Jun 21, 2023

Describe the bug
cyto_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:

  1. 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 = "*"
  2. Create a GatingTemplate object using gatingTemplate(path)
  3. 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
image
Error message from preprocess_csv. 'A' is the alias name. Missing space is an error in openCyto.

Desktop (please complete the following information):

  • OS: Linux
  • CytoExploreR version 1.1.0
  • OpenCyto version 2.9.4
@RSM151 RSM151 added the Bug Something isn't working label Jun 21, 2023
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