read.gatingML.cytobank fails on biaxial gates drawn on compensated/uncompensated axes

[bjreisman]

Thanks for your work on this package! I've run into the following issue: the read.gatingML.cytobank appears to fail when I attempt to read in an exported cytobank gatingML file with the following error message: (I'd be happy to share the gatingML file, but I'm not sure how to add attachments to github).

library(flowUtils)
library(CytoML)

file <-  "CytExp_29783_Gates_v5.xml"
gatingML.cytobank <- read.gatingML.cytobank(file)

Error in addGate(gateInfo, flowEnv, g, thisPopId, gateID) :
multiple gates found for Gate_1590224_dmlhYmxl

This gate corresponds to a polygon gate drawn against FSC and Ax700.
On inspecting the gatingML file, there appears to be only one Gate_1590224_dmlhYmxl defined.

<gating:PolygonGate gating:id="Gate_1590224_dmlhYmxl">
    <data-type:custom_info>
      <cytobank>
        <name>viable</name>
        <id>1590224</id>
        <gate_id>4</gate_id>
        <type>PolygonGate</type>
        <version>5</version>
        <compensation_id>3519</compensation_id>
        <fcs_file_id />
        <tailored>false</tailored>
        <tailored_per_population>false</tailored_per_population>
        <tailored_per_population_gateset_id />
        <fcs_file_filename />
        <definition>{"scale":{"x":{"flag":1,"argument":"1","min":1.0,"max":262144.0,"bins":256,"size":256},"y":{"flag":4,"argument":"1500","min":-4000.0,"max":262144.0,"bins":256,"size":256}},"positive":false,"negative":false,"label":[171153.05752893395,1.6602280372211227],"polygon":{"vertices":[[140789.0034748799,1.1618252220891794],[32490.54401542045,1.1618252220891794],[7187.1656370420715,0.48751553102831524],[17308.51698839342,-1.4181422915349964],[44636.165637042075,-1.8579094813572992],[179250.13861001504,-1.3888244788801762],[200504.9764478529,0.04774834120601246],[171153.05752893395,1.3670499106729208]]}}</definition>
      </cytobank>
    </data-type:custom_info>
    <gating:dimension gating:compensation-ref="uncompensated">
      <data-type:fcs-dimension data-type:name="FSC-A" />
    </gating:dimension>
    <gating:dimension gating:compensation-ref="Spill_3519" gating:transformation-ref="Tr_Arcsinh_1500"> 
      <data-type:fcs-dimension data-type:name="Comp_Alexa Fluor 700-A" />
    </gating:dimension>
    <gating:vertex>
      <gating:coordinate data-type:value="140789.0034748799" />
      <gating:coordinate data-type:value="1.1618252220891794" />
    </gating:vertex>
    <gating:vertex>
      <gating:coordinate data-type:value="32490.54401542045" />
      <gating:coordinate data-type:value="1.1618252220891794" />
    </gating:vertex>
    <gating:vertex>
      <gating:coordinate data-type:value="7187.1656370420715" />
      <gating:coordinate data-type:value="0.48751553102831524" />
    </gating:vertex>
    <gating:vertex>
      <gating:coordinate data-type:value="17308.51698839342" />
      <gating:coordinate data-type:value="-1.4181422915349964" />
    </gating:vertex>
    <gating:vertex>
      <gating:coordinate data-type:value="44636.165637042075" />
      <gating:coordinate data-type:value="-1.8579094813572992" />
    </gating:vertex>
    <gating:vertex>
      <gating:coordinate data-type:value="179250.13861001504" />
      <gating:coordinate data-type:value="-1.3888244788801762" />
    </gating:vertex>
    <gating:vertex>
      <gating:coordinate data-type:value="200504.9764478529" />
      <gating:coordinate data-type:value="0.04774834120601246" />
    </gating:vertex>
    <gating:vertex>
      <gating:coordinate data-type:value="171153.05752893395" />
      <gating:coordinate data-type:value="1.3670499106729208" />
    </gating:vertex>
  </gating:PolygonGate>

The flowUtils::read.gatingML function is able to read the gatingML file, and also only finds a single version of the gate in question:

flowEnv <- new.env()
gatingML <- read.gatingML(file, flowEnv)
table(grep("Gate_", names(flowEnv), value = T))

> table(grep("Gate_", names(flowEnv), value = T))
                Gate_1590221_aW50YWN0         Gate_1590222_c2luZ2xlcy1zc2M.         Gate_1590223_c2luZ2xlcy1mc2M.                 Gate_1590224_dmlhYmxl 
                                    1                                     1                                     1                                     1 
            Gate_1590225_YmFyY29kZWQ.                 Gate_1590226_cEJBQkU. Gate_1590227_cEJBQkUtSFJhc0cxMlYrSUwz Gate_1590228_cEJBQkUtSFJhc0cxMlYtSUwz 
                                    1                                     1                                     1                                     1 
Gate_1590229_cE1TQ1YtRUdGUl9MODU4Ug.. 
                                    1 

In my attempt to debug it, I believe the duplication is occurring within the parse.gateInfo() function: as can be seen here:

Browse[2]> gateInfo[,1:7]
                                       id               name gate_id fcs      comp_ref       trans_ref                                                 params
 1:                 Gate_1590221_aW50YWN0             intact       1     uncompensated                                                            SSC-A:FSC-A
 2:         Gate_1590222_c2luZ2xlcy1zc2M.        singles-ssc       2     uncompensated                                                            SSC-H:SSC-W
 3:         Gate_1590223_c2luZ2xlcy1mc2M.        singles-fsc       3     uncompensated                                                            FSC-W:FSC-H
 4:                 Gate_1590224_dmlhYmxl             viable       4     uncompensated Tr_Arcsinh_1500                           FSC-A:Comp_Alexa Fluor 700-A
 5:                 Gate_1590224_dmlhYmxl             viable       4        Spill_3519 Tr_Arcsinh_1500                           FSC-A:Comp_Alexa Fluor 700-A

It appears that the issue is that one of the gating axis is compensated (Ax700) while the other one is not (FSC-A), which the function interprets at there being two versions of the gate drawn on different compensation matrices.

[mikejiang]

You can zip and attach the xml

[bjreisman]

Thanks! See attached.
exampleGatingML.zip

[mikejiang]

@bjreisman , let me know if it resolves your issue.

[bjreisman]

The newest version worked! Thanks for the quick turnaround.