Compute congruence metrics between two taxonomic assignments
Source:R/tc_linked_trees.R
tc_congruence_metrics.Rd
Computes metrics quantifying the congruence between two taxonomic assignments for the same set of taxa (ASVs/OTUs). This is useful for comparing different taxonomic databases, assignment methods, or reference versions.
Arguments
- physeq_1
(required) A
phyloseq-classobject with the first taxonomic assignment.- physeq_2
(phyloseq, default NULL) A
phyloseq-classobject with the second taxonomic assignment. If NULL, uses physeq_1 (useful for comparing different rank columns from the same object).- ranks_1
(character vector, required) Taxonomic rank names to use for the first assignment. Must match column names in physeq_1's tax_table.
- ranks_2
(character vector, default NULL) Taxonomic rank names to use for the second assignment. Must match column names in physeq_2's tax_table. If NULL, uses the same ranks as ranks_1 vector.
Value
A list with the following components:
- summary
A data frame with counts and percentages for each category, including
leaf_match_congruencewhich counts taxa where the deepest classification matches regardless of the path- only_in_1
Character vector of taxa names present only in physeq_1
- only_in_2
Character vector of taxa names present only in physeq_2
- classified_only_1
Character vector of common taxa classified only in physeq_1 (all NA in physeq_2 for the specified ranks)
- classified_only_2
Character vector of common taxa classified only in physeq_2 (all NA in physeq_1 for the specified ranks)
- unclassified_both
Character vector of common taxa with all NA in both physeq objects
- total_congruent
Character vector of taxa with identical taxonomic paths (same values at all ranks, same NA positions)
- partial_1_deeper
Character vector of taxa where physeq_1 classifies to a deeper rank but agrees on shared ranks
- partial_2_deeper
Character vector of taxa where physeq_2 classifies to a deeper rank but agrees on shared ranks
- incongruent_leaves
Character vector of taxa with disagreement at the deepest (leaf) level where both have assignments
- incongruent_nodes
Character vector of taxa with disagreement at higher (internal node) levels, even if leaves match
- details
A data frame with per-taxon details including: taxon name, depth_1, depth_2, leaf_1, leaf_2, leaf_match (TRUE if leaves are equal), and category
Examples
# Compare two taxonomic assignments from the same phyloseq object
metrics <- tc_congruence_metrics(
subset_taxa(Glom_otu, Phyla == "Fungi" | Phylum__eukaryome_Glomero == "Fungi"),
ranks_1 = c("Phyla", "Class", "Order", "Family"),
ranks_2 = c(
"Phylum__eukaryome_Glomero", "Class__eukaryome_Glomero",
"Order__eukaryome_Glomero", "Family__eukaryome_Glomero"
)
)
# View summary
metrics$summary
#> category count percentage
#> 1 only_in_1 0 0.00
#> 2 only_in_2 0 0.00
#> 3 classified_only_1 0 0.00
#> 4 classified_only_2 0 0.00
#> 5 unclassified_both 0 0.00
#> 6 total_congruent 0 0.00
#> 7 leaf_match_congruence 111 9.68
#> 8 partial_1_deeper 0 0.00
#> 9 partial_2_deeper 0 0.00
#> 10 incongruent_leaves 673 58.67
#> 11 incongruent_nodes 474 41.33
# Get taxa with leaf-level incongruence
metrics$incongruent_leaves
#> [1] "Taxa_1" "Taxa_8" "Taxa_9" "Taxa_14" "Taxa_15" "Taxa_18"
#> [7] "Taxa_19" "Taxa_27" "Taxa_29" "Taxa_30" "Taxa_31" "Taxa_35"
#> [13] "Taxa_37" "Taxa_52" "Taxa_57" "Taxa_58" "Taxa_60" "Taxa_61"
#> [19] "Taxa_65" "Taxa_66" "Taxa_67" "Taxa_68" "Taxa_69" "Taxa_70"
#> [25] "Taxa_72" "Taxa_73" "Taxa_77" "Taxa_79" "Taxa_80" "Taxa_86"
#> [31] "Taxa_87" "Taxa_90" "Taxa_94" "Taxa_95" "Taxa_101" "Taxa_102"
#> [37] "Taxa_106" "Taxa_108" "Taxa_109" "Taxa_110" "Taxa_111" "Taxa_113"
#> [43] "Taxa_115" "Taxa_123" "Taxa_126" "Taxa_128" "Taxa_129" "Taxa_132"
#> [49] "Taxa_136" "Taxa_137" "Taxa_139" "Taxa_140" "Taxa_143" "Taxa_145"
#> [55] "Taxa_147" "Taxa_148" "Taxa_151" "Taxa_157" "Taxa_166" "Taxa_175"
#> [61] "Taxa_179" "Taxa_181" "Taxa_184" "Taxa_185" "Taxa_187" "Taxa_194"
#> [67] "Taxa_195" "Taxa_200" "Taxa_204" "Taxa_207" "Taxa_214" "Taxa_222"
#> [73] "Taxa_223" "Taxa_228" "Taxa_229" "Taxa_234" "Taxa_235" "Taxa_236"
#> [79] "Taxa_246" "Taxa_248" "Taxa_252" "Taxa_257" "Taxa_259" "Taxa_263"
#> [85] "Taxa_266" "Taxa_269" "Taxa_271" "Taxa_274" "Taxa_285" "Taxa_288"
#> [91] "Taxa_289" "Taxa_292" "Taxa_293" "Taxa_294" "Taxa_301" "Taxa_304"
#> [97] "Taxa_305" "Taxa_309" "Taxa_310" "Taxa_312" "Taxa_313" "Taxa_316"
#> [103] "Taxa_317" "Taxa_318" "Taxa_322" "Taxa_328" "Taxa_329" "Taxa_339"
#> [109] "Taxa_341" "Taxa_342" "Taxa_345" "Taxa_346" "Taxa_348" "Taxa_352"
#> [115] "Taxa_354" "Taxa_357" "Taxa_358" "Taxa_362" "Taxa_364" "Taxa_367"
#> [121] "Taxa_378" "Taxa_379" "Taxa_390" "Taxa_402" "Taxa_403" "Taxa_407"
#> [127] "Taxa_408" "Taxa_412" "Taxa_418" "Taxa_419" "Taxa_420" "Taxa_422"
#> [133] "Taxa_427" "Taxa_433" "Taxa_440" "Taxa_443" "Taxa_450" "Taxa_453"
#> [139] "Taxa_454" "Taxa_459" "Taxa_460" "Taxa_465" "Taxa_480" "Taxa_483"
#> [145] "Taxa_484" "Taxa_485" "Taxa_489" "Taxa_498" "Taxa_503" "Taxa_507"
#> [151] "Taxa_509" "Taxa_510" "Taxa_511" "Taxa_521" "Taxa_526" "Taxa_532"
#> [157] "Taxa_535" "Taxa_541" "Taxa_547" "Taxa_549" "Taxa_551" "Taxa_556"
#> [163] "Taxa_557" "Taxa_558" "Taxa_561" "Taxa_569" "Taxa_570" "Taxa_574"
#> [169] "Taxa_583" "Taxa_585" "Taxa_588" "Taxa_596" "Taxa_597" "Taxa_598"
#> [175] "Taxa_599" "Taxa_600" "Taxa_603" "Taxa_604" "Taxa_605" "Taxa_608"
#> [181] "Taxa_610" "Taxa_611" "Taxa_619" "Taxa_625" "Taxa_626" "Taxa_630"
#> [187] "Taxa_632" "Taxa_635" "Taxa_640" "Taxa_648" "Taxa_650" "Taxa_658"
#> [193] "Taxa_659" "Taxa_660" "Taxa_662" "Taxa_665" "Taxa_668" "Taxa_669"
#> [199] "Taxa_670" "Taxa_673" "Taxa_682" "Taxa_695" "Taxa_696" "Taxa_702"
#> [205] "Taxa_707" "Taxa_708" "Taxa_709" "Taxa_711" "Taxa_715" "Taxa_729"
#> [211] "Taxa_730" "Taxa_733" "Taxa_745" "Taxa_747" "Taxa_751" "Taxa_755"
#> [217] "Taxa_759" "Taxa_766" "Taxa_769" "Taxa_774" "Taxa_776" "Taxa_789"
#> [223] "Taxa_795" "Taxa_796" "Taxa_797" "Taxa_806" "Taxa_807" "Taxa_809"
#> [229] "Taxa_811" "Taxa_820" "Taxa_826" "Taxa_828" "Taxa_850" "Taxa_856"
#> [235] "Taxa_860" "Taxa_865" "Taxa_866" "Taxa_876" "Taxa_881" "Taxa_888"
#> [241] "Taxa_898" "Taxa_899" "Taxa_901" "Taxa_902" "Taxa_903" "Taxa_932"
#> [247] "Taxa_933" "Taxa_934" "Taxa_950" "Taxa_955" "Taxa_966" "Taxa_968"
#> [253] "Taxa_969" "Taxa_971" "Taxa_973" "Taxa_983" "Taxa_992" "Taxa_995"
#> [259] "Taxa_996" "Taxa_1001" "Taxa_1008" "Taxa_1020" "Taxa_1021" "Taxa_1023"
#> [265] "Taxa_1026" "Taxa_1031" "Taxa_1033" "Taxa_1036" "Taxa_1041" "Taxa_1055"
#> [271] "Taxa_1071" "Taxa_1074" "Taxa_1075" "Taxa_1086" "Taxa_1093" "Taxa_1101"
#> [277] "Taxa_1113" "Taxa_1121" "Taxa_1125" "Taxa_1135" "Taxa_1142" "Taxa_1150"
#> [283] "Taxa_1152" "Taxa_1160" "Taxa_1161" "Taxa_1167" "Taxa_1168" "Taxa_1180"
#> [289] "Taxa_1187" "Taxa_1193" "Taxa_1195" "Taxa_1210" "Taxa_1217" "Taxa_1233"
#> [295] "Taxa_1236" "Taxa_1248" "Taxa_1252" "Taxa_1258" "Taxa_1263" "Taxa_1265"
#> [301] "Taxa_1274" "Taxa_1276" "Taxa_1277" "Taxa_1279" "Taxa_1286" "Taxa_1294"
#> [307] "Taxa_1296" "Taxa_1297" "Taxa_1304" "Taxa_1311" "Taxa_1327" "Taxa_1329"
#> [313] "Taxa_1335" "Taxa_1353" "Taxa_1374" "Taxa_1381" "Taxa_1382" "Taxa_1385"
#> [319] "Taxa_1387" "Taxa_1388" "Taxa_1390" "Taxa_1391" "Taxa_1424" "Taxa_1430"
#> [325] "Taxa_1432" "Taxa_1433" "Taxa_1436" "Taxa_1437" "Taxa_1449" "Taxa_1453"
#> [331] "Taxa_1465" "Taxa_1471" "Taxa_1474" "Taxa_1481" "Taxa_1484" "Taxa_1499"
#> [337] "Taxa_1501" "Taxa_1504" "Taxa_1521" "Taxa_1527" "Taxa_1529" "Taxa_1536"
#> [343] "Taxa_1546" "Taxa_1553" "Taxa_1558" "Taxa_1564" "Taxa_1573" "Taxa_1585"
#> [349] "Taxa_1591" "Taxa_1600" "Taxa_1608" "Taxa_1629" "Taxa_1635" "Taxa_1660"
#> [355] "Taxa_1681" "Taxa_1693" "Taxa_1699" "Taxa_1711" "Taxa_1719" "Taxa_1723"
#> [361] "Taxa_1741" "Taxa_1745" "Taxa_1756" "Taxa_1768" "Taxa_1770" "Taxa_1783"
#> [367] "Taxa_1793" "Taxa_1795" "Taxa_1804" "Taxa_1818" "Taxa_1821" "Taxa_1823"
#> [373] "Taxa_1830" "Taxa_1832" "Taxa_1834" "Taxa_1852" "Taxa_1853" "Taxa_1857"
#> [379] "Taxa_1873" "Taxa_1874" "Taxa_1879" "Taxa_1882" "Taxa_1892" "Taxa_1898"
#> [385] "Taxa_1904" "Taxa_1909" "Taxa_1912" "Taxa_1914" "Taxa_1915" "Taxa_1920"
#> [391] "Taxa_1930" "Taxa_1960" "Taxa_1962" "Taxa_1977" "Taxa_1988" "Taxa_1999"
#> [397] "Taxa_2008" "Taxa_2021" "Taxa_2044" "Taxa_2047" "Taxa_2054" "Taxa_2072"
#> [403] "Taxa_2081" "Taxa_2102" "Taxa_2108" "Taxa_2114" "Taxa_2118" "Taxa_2131"
#> [409] "Taxa_2134" "Taxa_2143" "Taxa_2155" "Taxa_2164" "Taxa_2171" "Taxa_2172"
#> [415] "Taxa_2201" "Taxa_2205" "Taxa_2227" "Taxa_2239" "Taxa_2242" "Taxa_2247"
#> [421] "Taxa_2253" "Taxa_2256" "Taxa_2270" "Taxa_2279" "Taxa_2297" "Taxa_2299"
#> [427] "Taxa_2302" "Taxa_2304" "Taxa_2315" "Taxa_2316" "Taxa_2342" "Taxa_2351"
#> [433] "Taxa_2360" "Taxa_2367" "Taxa_2371" "Taxa_2374" "Taxa_2386" "Taxa_2411"
#> [439] "Taxa_2415" "Taxa_2426" "Taxa_2435" "Taxa_2440" "Taxa_2443" "Taxa_2444"
#> [445] "Taxa_2472" "Taxa_2493" "Taxa_2530" "Taxa_2536" "Taxa_2541" "Taxa_2549"
#> [451] "Taxa_2553" "Taxa_2559" "Taxa_2566" "Taxa_2574" "Taxa_2589" "Taxa_2603"
#> [457] "Taxa_2611" "Taxa_2614" "Taxa_2626" "Taxa_2631" "Taxa_2637" "Taxa_2639"
#> [463] "Taxa_2640" "Taxa_2644" "Taxa_2654" "Taxa_2663" "Taxa_2680" "Taxa_2682"
#> [469] "Taxa_2698" "Taxa_2706" "Taxa_2708" "Taxa_2734" "Taxa_2742" "Taxa_2749"
#> [475] "Taxa_2754" "Taxa_2766" "Taxa_2768" "Taxa_2777" "Taxa_2778" "Taxa_2780"
#> [481] "Taxa_2793" "Taxa_2807" "Taxa_2811" "Taxa_2812" "Taxa_2813" "Taxa_2818"
#> [487] "Taxa_2819" "Taxa_2830" "Taxa_2833" "Taxa_2834" "Taxa_2839" "Taxa_3201"
#> [493] "Taxa_2857" "Taxa_2859" "Taxa_2861" "Taxa_2870" "Taxa_2875" "Taxa_2885"
#> [499] "Taxa_2886" "Taxa_2889" "Taxa_2902" "Taxa_2904" "Taxa_2906" "Taxa_2908"
#> [505] "Taxa_2911" "Taxa_2912" "Taxa_2929" "Taxa_2930" "Taxa_2934" "Taxa_2938"
#> [511] "Taxa_2945" "Taxa_2951" "Taxa_2954" "Taxa_2962" "Taxa_2970" "Taxa_2973"
#> [517] "Taxa_2998" "Taxa_2999" "Taxa_3000" "Taxa_3021" "Taxa_3024" "Taxa_3031"
#> [523] "Taxa_3041" "Taxa_3045" "Taxa_3047" "Taxa_3048" "Taxa_3055" "Taxa_3059"
#> [529] "Taxa_3073" "Taxa_3087" "Taxa_3099" "Taxa_3103" "Taxa_3108" "Taxa_3110"
#> [535] "Taxa_3118" "Taxa_3124" "Taxa_3134" "Taxa_3141" "Taxa_3149" "Taxa_3157"
#> [541] "Taxa_3158" "Taxa_3188" "Taxa_3190" "Taxa_3198" "Taxa_3207" "Taxa_3209"
#> [547] "Taxa_3213" "Taxa_3216" "Taxa_3217" "Taxa_3220" "Taxa_3229" "Taxa_3230"
#> [553] "Taxa_3244" "Taxa_3264" "Taxa_3265" "Taxa_3267" "Taxa_3274" "Taxa_3275"
#> [559] "Taxa_3276" "Taxa_3277" "Taxa_3278" "Taxa_3290" "Taxa_3291" "Taxa_3300"
#> [565] "Taxa_3308" "Taxa_3310" "Taxa_3312" "Taxa_3314" "Taxa_3319" "Taxa_3328"
#> [571] "Taxa_3331" "Taxa_3338" "Taxa_3339" "Taxa_3341" "Taxa_3342" "Taxa_3346"
#> [577] "Taxa_3347" "Taxa_3348" "Taxa_3355" "Taxa_3356" "Taxa_3359" "Taxa_3360"
#> [583] "Taxa_3361" "Taxa_3363" "Taxa_3365" "Taxa_3372" "Taxa_3375" "Taxa_3379"
#> [589] "Taxa_3387" "Taxa_3388" "Taxa_3389" "Taxa_3390" "Taxa_3394" "Taxa_3398"
#> [595] "Taxa_3401" "Taxa_3402" "Taxa_3403" "Taxa_3405" "Taxa_3415" "Taxa_3417"
#> [601] "Taxa_3422" "Taxa_3428" "Taxa_3436" "Taxa_3438" "Taxa_3439" "Taxa_3445"
#> [607] "Taxa_3446" "Taxa_3447" "Taxa_3450" "Taxa_3451" "Taxa_3455" "Taxa_3456"
#> [613] "Taxa_3458" "Taxa_3465" "Taxa_3466" "Taxa_3469" "Taxa_3470" "Taxa_3471"
#> [619] "Taxa_3474" "Taxa_3478" "Taxa_3482" "Taxa_3486" "Taxa_3488" "Taxa_3490"
#> [625] "Taxa_3493" "Taxa_3496" "Taxa_3506" "Taxa_3509" "Taxa_3512" "Taxa_3529"
#> [631] "Taxa_3531" "Taxa_3549" "Taxa_3550" "Taxa_3552" "Taxa_3558" "Taxa_3566"
#> [637] "Taxa_3567" "Taxa_3571" "Taxa_3572" "Taxa_3574" "Taxa_3576" "Taxa_3577"
#> [643] "Taxa_3578" "Taxa_3602" "Taxa_3613" "Taxa_3614" "Taxa_3619" "Taxa_3620"
#> [649] "Taxa_3622" "Taxa_3624" "Taxa_3626" "Taxa_3629" "Taxa_3635" "Taxa_3637"
#> [655] "Taxa_3640" "Taxa_3645" "Taxa_3646" "Taxa_3647" "Taxa_3649" "Taxa_3650"
#> [661] "Taxa_3654" "Taxa_3661" "Taxa_3664" "Taxa_3666" "Taxa_3671" "Taxa_3672"
#> [667] "Taxa_3673" "Taxa_3676" "Taxa_3677" "Taxa_3678" "Taxa_3692" "Taxa_3693"
#> [673] "Taxa_3697"