hubmapconsortium/ccf-asct-reporter

Support for BProtein +/- intermediate values in visualization and reports

emquardokus opened this issue · 0 comments

Problem: Flow cytometry reported BProtein values can be + (positive) , - (negative) or +/- (intermediate).
Currently the Reporter supports + or - but not +/-
The visualization shows for lymph node table v1.2 Vimentin +/ in the visualization because in the ASCT+B table it has an intermediate value : vimentin +/-
Spoke with @bherr2 4-26-2023 regarding the issue.
Support Need: represent +/- (intermediate) from ASCT+B tables for BProtein in visualization and reports
Thoughts: on implementation
Currently check for end value of + or - for protein biomarkers in ASCT+B tables, need to extend to +/-
Bruce 10:14 AM
This is what we report in the data currently:

export enum PROTEIN_PRESENCE {
POS = 'Positive',
NEG = 'Negative',
UNKNOWN = 'Unknown'
}

  • @pbrm4 Bruce 10:43 AM
    Ok, Pramod will just need to update this to check for +/- on the data side:
    const hasPos = name.endsWith('+');
    const hasNeg = name.endsWith('-');
    if (hasPos) {
    this.name = name.slice(0, -1);
    this.proteinPresence = PROTEIN_PRESENCE.POS;
    } else if (hasNeg) {
    this.name = name.slice(0, -1);
    this.proteinPresence = PROTEIN_PRESENCE.NEG;
    } else {
    this.proteinPresence = PROTEIN_PRESENCE.UNKNOWN;
    }

    Visualization
    -In the visualization + (positive) renders as a blue line connecting cell type to BProtein, - (negative) renders as a red line connecting cell type to BProtein.
  • We discussed and since red + blue = purple that this could be the line color for +/- (intermediate)?
  • This would also need to be added to the upper left "Legend".