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RGLab / CytoML

A GatingML Interface for Cross Platform Cytometry Data Sharing
GNU Affero General Public License v3.0
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skip the faulty gates without failing to parse the rest of gating tree #96

Closed mikejiang closed 4 years ago

mikejiang commented 4 years ago

Sometime there is some issue associated with parsing a particular gate (or node) in flowJo workspace (due to various reasons). Right now it will simply stop parsing and throw the error. e.g.

> flowjo_to_gatingset(ws, name = 4)
 Error in (function (ws, group_id, subset, execute, path, h5_dir, includeGates,  : 
  colname not found: <wrong-A>

It is helpful to be able to skip that gate (and its descendants) so that the rest of gating tree can still be parsed and gated properly.

mikejiang commented 4 years ago

With the patch, passing skip_faulty_gate argument to skip the faulty node.

   gs <- flowjo_to_gatingset(ws, name = 4, skip_faulty_gate = TRUE)
colname not found: <wrong-A>
 Skipping the faulty node CD4 and its descendants 

> gh_pop_get_stats(gs[[1]])
                                          pop  count
 1:                                      root 119531
 2:                               /not debris  91720
 3:                      /not debris/singlets  87022
 4:                 /not debris/singlets/CD3+  54483
 5:             /not debris/singlets/CD3+/CD4     NA
 6:     /not debris/singlets/CD3+/CD4/38- DR+     NA
 7:     /not debris/singlets/CD3+/CD4/38+ DR+     NA
 8:     /not debris/singlets/CD3+/CD4/38+ DR-     NA
 9:     /not debris/singlets/CD3+/CD4/38- DR-     NA
10: /not debris/singlets/CD3+/CD4/CCR7- 45RA+     NA
11: /not debris/singlets/CD3+/CD4/CCR7+ 45RA+     NA
12: /not debris/singlets/CD3+/CD4/CCR7+ 45RA-     NA
13: /not debris/singlets/CD3+/CD4/CCR7- 45RA-     NA
14:             /not debris/singlets/CD3+/CD8  14564
15:     /not debris/singlets/CD3+/CD8/38- DR+   1308
16:     /not debris/singlets/CD3+/CD8/38+ DR+   1335
17:     /not debris/singlets/CD3+/CD8/38+ DR-   4450
18:     /not debris/singlets/CD3+/CD8/38- DR-   7471
19: /not debris/singlets/CD3+/CD8/CCR7- 45RA+   3919
20: /not debris/singlets/CD3+/CD8/CCR7+ 45RA+   6802
21: /not debris/singlets/CD3+/CD8/CCR7+ 45RA-   1569
22: /not debris/singlets/CD3+/CD8/CCR7- 45RA-   2274
23:             /not debris/singlets/CD3+/DNT   1293
24:             /not debris/singlets/CD3+/DPT    819