Can't color tips and nodes by trait

Issue #2 resolved
Tartu Immunology created an issue

Dear Immcantation Team,

I’m trying to color the trees by a C gene call. Here’s how the trees were built:

dowser_clones <- all_clones |>
    filter(sample_name == 'sample1') |>
    formatClones(
        traits = c('c_call_simplified'),
        num_fields = c('duplicate_count'), 
        columns = c('sample_name'),
        nproc = 4
    )
custom_palette = getPalette(c(ISOTYPE_LEVELS, 'Germline'), 'Paired')
trees <- dowser_clones |>
    getTrees(
        build = 'dnapars',
        id = sample(1:10e10, 1),
        exec = '~/bin/phylip-3.697/exe/dnapars',
        trait = 'c_call_simplified',
        #palette = custom_palette,
        nproc = 4
    )
plots <- plotTrees(
    trees[1:10,],
    tips = 'c_call_simplified',
    tip_palette = custom_palette,
    tipsize = 'duplicate_count'
)

all_clones is a data frame in AIRR format with a column called c_call_simplified that has the C gene call.

I get the following error:

Error in plotTrees(trees[1:10, ], tips = "c_call_simplified", tip_palette = custom_palette, : 1 not found in tip_palette2 not found in tip_palette4 not found in tip_palette6 not found in tip_palette3 not found in tip_palette8 not found in tip_palette5 not found in tip_palette7 not found in tip_palette
Traceback:

1. plotTrees(trees[1:10, ], tips = "c_call_simplified", tip_palette = custom_palette, 
 .     tipsize = "duplicate_count")
2. stop(paste(nfound, "not found in tip_palette"))

custom_palette is:

IGHM'#A6CEE3'IGHD'#1F78B4'IGHG3'#B2DF8A'IGHG1'#33A02C'IGHA1'#FB9A99'IGHG2'#E31A1C'IGHG4'#FDBF6F'IGHE'#FF7F00'IGHA2'#CAB2D6'Germline'#6A3D9A'

When I replace custom_palette with simply 'Paired' I get a tree where all tips are of the same color:

Would appreciate any tips suggestions.

Comments (2)

  1. Kenneth Hoehn

    Hey sorry for the slow reply. Is c_call_simplified stored as a factor? Seems like it’s using integers rather than strings as states for some reason. If so it’s best to convert it to a character before formatting the clones. Also, if you’re using ape 5.5, it’s best to update to the latest version, since we’ve had issues with 5.5 recently.

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