{ "cells": [ { "cell_type": "code", "execution_count": 23, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "200" ] }, "execution_count": 23, "metadata": {}, "output_type": "execute_result" } ], "source": [ "using DataFrames\n", "using StatsPlots\n", "using CSV\n", "using FASTX\n", "ENV[\"COLUMNS\"] = 200" ] }, { "cell_type": "code", "execution_count": 24, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
sample | Clade | Order | Family | Species | Tissue Type | Contamination | numprot | |
---|---|---|---|---|---|---|---|---|
String | String | String | String | String | String? | String? | Int64 | |
1 | AALA | Basal Eudicots | Sabiales | Sabiaceae | Meliosma cuneifolia | leaves | All confirmed to Genus level! | 17784 |
2 | AAXJ | Core Eudicots | Caryophyllales | Chenopodiaceae | Atriplex prostrata | missing | missing | 17406 |
3 | ABCD | Mosses | Grimmiales | Grimmiaceae | Racomitrium elongatum | gametophyte | All confirmed to Species level! | 16274 |
4 | ABEH | Core Eudicots/Asterids | incertae sedis | Boraginaceae | Heliotropium greggii | mature leaf | All confirmed to Family level! | 18864 |
5 | ABIJ | Lycophytes | Selaginellales | Selaginellaceae | Selaginella lepidophylla | Young fronds | All confirmed to Genus level! | 14486 |
6 | ABSS | Magnoliids | Laurales | Lauraceae | Sassafras albidum | young leaves | Harmless Contamination | 21046 |
7 | ACFP | Core Eudicots/Rosids | Rosales | Urticaceae | Boehmeria nivea | shoot apex including nascent leaves and woody stem | All confirmed to Species level! | 12474 |
8 | ACRY | Green Algae | Volvocales | Phacotaceae | Pteromonas sp. | algal cells | All confirmed to Genus level! | 6862 |
9 | ACWS | Conifers | Pinales | Araucariaceae | Araucaria sp. | Young Leaf | Harmless Contamination | 17670 |
10 | ACYX | Basal Eudicots | Ranunculales | Papaveraceae | Papaver rhoeas | leaf | Harmless Contamination | 20671 |
11 | ADHK | Core Eudicots/Asterids | Ericales | Diapensiaceae | Galax urceolata | leaves - diploid | Harmless Contamination | 18278 |
12 | AEKF | Green Algae | Zygnematales | Peniaceae | mixed species | algal cells | Harmless Contamination | 6429 |
13 | AEPI | Core Eudicots/Rosids | Malpighiales | Linaceae | Linum leonii | stem apex, shoot, leaves | All confirmed to Genus level! | 19260 |
14 | AEXY | Liverworts | Blasiales | Blasiaceae | Blasia sp. | whole plant | Harmless Contamination | 17511 |
15 | AFLV | Monocots | Liliales | Melanthiaceae | Xerophyllum asphodeloides | vegetative shoot | Harmless Contamination | 20258 |
16 | AFPO | Leptosporangiate Monilophytes | Polypodiales | Athyriaceae | Athyrium sp. | gametophyte | Harmless Contamination | 17235 |
17 | AFQQ | Core Eudicots/Asterids | Asterales | Asteraceae | Inula helenium | leaves and root | Harmless Contamination | 17139 |
18 | AGIO | Green Algae | Volvocales | Haematococcaceae | Haematococcus pluvialis | algal cells | Harmless Contamination | 8252 |
19 | AHRN | Core Eudicots/Asterids | Solanales | Convolvulaceae | Cuscuta pentagona | leaves | Harmless Contamination | 18200 |
20 | AIGO | Conifers | Pinales | Cupressaceae | Chamaecyparis lawsoniana | leaf | All confirmed to Genus level! | 18173 |
21 | AIOU | Core Eudicots/Asterids | Solanales | Solanaceae | Brugmansia sanguinea | young shoot | Harmless Contamination | 21929 |
22 | AJAU | Green Algae | Chaetophorales | Chaetophoraceae | Helicodictyon planctonicum | algal cells | missing | 7676 |
23 | AJBK | Core Eudicots/Rosids | Myrtales | Onagraceae | Oenothera elata | 4th true leaf | All confirmed to Genus level! | 19837 |
24 | AJFN | Core Eudicots/Asterids | Apiales | Myodocarpaceae | Myodocarpus sp. | 0 | Harmless Contamination | 25965 |
25 | AJJE | Core Eudicots/Rosids | Myrtales | Combretaceae | Terminalia neotaliala | leaves | Harmless Contamination | 15840 |
26 | AJUW | Green Algae | Volvocales | Chlamydomonadaceae | Chloromonas rosae | algal cells | All confirmed to Species level! | 11355 |
27 | AKCR | Green Algae | Chlorellales | Chlorellaceae | Parachlorella kessleri | algal cells | All confirmed to Species level! | 7640 |
28 | AKRH | Core Eudicots/Rosids | Fabales | Fabaceae | Glycine soja | DB root + NaHCO3 | Harmless Contamination | 30320 |
29 | AKTA | Core Eudicots | Caryophyllales | Chenopodiaceae | Atriplex hortensis | mature leaf | All confirmed to Family level! | 16041 |
30 | AKXB | Hornworts | Dendrocerotales | Dendrocerotaceae | Phaeomegaceros coriaceus | sporophyte | missing | 14168 |
⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ |
GroupedDataFrame with 894 groups based on key: Species
First Group (1 row): Species = \"Meliosma cuneifolia\"
sample | Clade | Order | Family | Species | Tissue Type | Contamination | numprot | |
---|---|---|---|---|---|---|---|---|
String | String | String | String | String | String? | String? | Int64 | |
1 | AALA | Basal Eudicots | Sabiales | Sabiaceae | Meliosma cuneifolia | leaves | All confirmed to Genus level! | 17784 |
⋮
Last Group (1 row): Species = \"Selaginella stauntoniana\"
sample | Clade | Order | Family | Species | Tissue Type | Contamination | numprot | |
---|---|---|---|---|---|---|---|---|
String | String | String | String | String | String? | String? | Int64 | |
1 | ZZOL | Lycophytes | Selaginellales | Selaginellaceae | Selaginella stauntoniana | Sterile and fertile material, and gemmae | Harmless Contamination | 15017 |
sample | Clade | Order | Family | Species | Tissue Type | Contamination | numprot | target | tlen | fullscore | domscore | hmmfrom | hmmto | alen | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
String | String | String | String | String | String? | String? | Int64 | String | Int64 | Float64 | Float64 | Int64 | Int64 | Int64 | |
1 | AALA | Basal Eudicots | Sabiales | Sabiaceae | Meliosma cuneifolia | leaves | All confirmed to Genus level! | 17784 | 6453 | 455 | 323.2 | 295.5 | 98 | 465 | 367 |
2 | AALA | Basal Eudicots | Sabiales | Sabiaceae | Meliosma cuneifolia | leaves | All confirmed to Genus level! | 17784 | 6453 | 455 | 323.2 | 25.5 | 151 | 207 | 56 |
3 | AALA | Basal Eudicots | Sabiales | Sabiaceae | Meliosma cuneifolia | leaves | All confirmed to Genus level! | 17784 | 14562 | 382 | 290.2 | 240.1 | 140 | 456 | 316 |
4 | AALA | Basal Eudicots | Sabiales | Sabiaceae | Meliosma cuneifolia | leaves | All confirmed to Genus level! | 17784 | 14562 | 382 | 290.2 | 55.7 | 146 | 300 | 154 |
5 | AALA | Basal Eudicots | Sabiales | Sabiaceae | Meliosma cuneifolia | leaves | All confirmed to Genus level! | 17784 | 14958 | 511 | 282.2 | 177.5 | 222 | 442 | 220 |
6 | AALA | Basal Eudicots | Sabiales | Sabiaceae | Meliosma cuneifolia | leaves | All confirmed to Genus level! | 17784 | 14958 | 511 | 282.2 | 52.9 | 208 | 325 | 117 |
7 | AALA | Basal Eudicots | Sabiales | Sabiaceae | Meliosma cuneifolia | leaves | All confirmed to Genus level! | 17784 | 14958 | 511 | 282.2 | 63.5 | 599 | 753 | 154 |
8 | AALA | Basal Eudicots | Sabiales | Sabiaceae | Meliosma cuneifolia | leaves | All confirmed to Genus level! | 17784 | 7097 | 537 | 242.1 | 92.7 | 75 | 247 | 172 |
9 | AALA | Basal Eudicots | Sabiales | Sabiaceae | Meliosma cuneifolia | leaves | All confirmed to Genus level! | 17784 | 7097 | 537 | 242.1 | 149.4 | 150 | 368 | 218 |
10 | AALA | Basal Eudicots | Sabiales | Sabiaceae | Meliosma cuneifolia | leaves | All confirmed to Genus level! | 17784 | 13815 | 349 | 238.1 | 233.0 | 111 | 443 | 332 |
11 | AALA | Basal Eudicots | Sabiales | Sabiaceae | Meliosma cuneifolia | leaves | All confirmed to Genus level! | 17784 | 79123 | 476 | 237.6 | 57.5 | 15 | 200 | 185 |
12 | AALA | Basal Eudicots | Sabiales | Sabiaceae | Meliosma cuneifolia | leaves | All confirmed to Genus level! | 17784 | 79123 | 476 | 237.6 | 188.4 | 130 | 398 | 268 |
13 | AALA | Basal Eudicots | Sabiales | Sabiaceae | Meliosma cuneifolia | leaves | All confirmed to Genus level! | 17784 | 14508 | 511 | 232.9 | 232.3 | 123 | 507 | 384 |
14 | AALA | Basal Eudicots | Sabiales | Sabiaceae | Meliosma cuneifolia | leaves | All confirmed to Genus level! | 17784 | 14638 | 398 | 227.6 | 146.6 | 190 | 387 | 197 |
15 | AALA | Basal Eudicots | Sabiales | Sabiaceae | Meliosma cuneifolia | leaves | All confirmed to Genus level! | 17784 | 14638 | 398 | 227.6 | 87.1 | 217 | 345 | 128 |
16 | AALA | Basal Eudicots | Sabiales | Sabiaceae | Meliosma cuneifolia | leaves | All confirmed to Genus level! | 17784 | 13525 | 425 | 197.4 | 164.8 | 120 | 436 | 316 |
17 | AALA | Basal Eudicots | Sabiales | Sabiaceae | Meliosma cuneifolia | leaves | All confirmed to Genus level! | 17784 | 13525 | 425 | 197.4 | 40.9 | 298 | 400 | 102 |
18 | AALA | Basal Eudicots | Sabiales | Sabiaceae | Meliosma cuneifolia | leaves | All confirmed to Genus level! | 17784 | 14184 | 423 | 188.4 | 107.4 | 259 | 444 | 185 |
19 | AALA | Basal Eudicots | Sabiales | Sabiaceae | Meliosma cuneifolia | leaves | All confirmed to Genus level! | 17784 | 14184 | 423 | 188.4 | 80.6 | 595 | 752 | 157 |
20 | AALA | Basal Eudicots | Sabiales | Sabiaceae | Meliosma cuneifolia | leaves | All confirmed to Genus level! | 17784 | 77185 | 269 | 187.3 | 94.2 | 350 | 467 | 117 |
21 | AALA | Basal Eudicots | Sabiales | Sabiaceae | Meliosma cuneifolia | leaves | All confirmed to Genus level! | 17784 | 77185 | 269 | 187.3 | 94.9 | 218 | 370 | 152 |
22 | AALA | Basal Eudicots | Sabiales | Sabiaceae | Meliosma cuneifolia | leaves | All confirmed to Genus level! | 17784 | 79175 | 445 | 186.5 | 91.8 | 269 | 390 | 121 |
23 | AALA | Basal Eudicots | Sabiales | Sabiaceae | Meliosma cuneifolia | leaves | All confirmed to Genus level! | 17784 | 79175 | 445 | 186.5 | 100.4 | 270 | 477 | 207 |
24 | AALA | Basal Eudicots | Sabiales | Sabiaceae | Meliosma cuneifolia | leaves | All confirmed to Genus level! | 17784 | 14870 | 653 | 180.6 | 89.9 | 205 | 454 | 249 |
25 | AALA | Basal Eudicots | Sabiales | Sabiaceae | Meliosma cuneifolia | leaves | All confirmed to Genus level! | 17784 | 14870 | 653 | 180.6 | 94.8 | 167 | 376 | 209 |
26 | AALA | Basal Eudicots | Sabiales | Sabiaceae | Meliosma cuneifolia | leaves | All confirmed to Genus level! | 17784 | 75923 | 193 | 177.2 | 60.7 | 233 | 301 | 68 |
27 | AALA | Basal Eudicots | Sabiales | Sabiaceae | Meliosma cuneifolia | leaves | All confirmed to Genus level! | 17784 | 75923 | 193 | 177.2 | 121.2 | 157 | 306 | 149 |
28 | AALA | Basal Eudicots | Sabiales | Sabiaceae | Meliosma cuneifolia | leaves | All confirmed to Genus level! | 17784 | 7989 | 411 | 154.6 | 154.2 | 175 | 439 | 264 |
29 | AALA | Basal Eudicots | Sabiales | Sabiaceae | Meliosma cuneifolia | leaves | All confirmed to Genus level! | 17784 | 78957 | 398 | 149.4 | 149.2 | 2 | 374 | 372 |
30 | AALA | Basal Eudicots | Sabiales | Sabiaceae | Meliosma cuneifolia | leaves | All confirmed to Genus level! | 17784 | 77610 | 278 | 145.9 | 145.7 | 208 | 472 | 264 |
⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ |
target | tlen | fullscore | domscore | hmmfrom | hmmto | alen | |
---|---|---|---|---|---|---|---|
String | Int64 | Float64 | Float64 | Int64 | Int64 | Int64 | |
1 | XP_010267950 | 868 | 1380.0 | 1379.8 | 1 | 762 | 761 |
2 | RVX01505 | 905 | 1374.5 | 1374.3 | 1 | 762 | 761 |
3 | TXG63280 | 878 | 1362.8 | 1362.6 | 1 | 762 | 761 |
4 | GBYR01007015.1_R_3773064 | 896 | 1359.7 | 1359.5 | 1 | 762 | 761 |
5 | XP_031274127 | 877 | 1354.8 | 1354.6 | 1 | 762 | 761 |
6 | XP_042492464 | 859 | 1352.1 | 1351.9 | 1 | 762 | 761 |
7 | XP_007051141 | 866 | 1348.6 | 1348.4 | 1 | 762 | 761 |
8 | XP_012082926 | 871 | 1348.5 | 1348.3 | 1 | 762 | 761 |
9 | KAF9834297 | 878 | 1348.5 | 1348.3 | 1 | 762 | 761 |
10 | GBJU01025666.1_F_12628 | 876 | 1347.6 | 1347.5 | 1 | 762 | 761 |
11 | PIA61046 | 876 | 1342.2 | 1342.0 | 1 | 762 | 761 |
12 | XP_021612152 | 875 | 1331.1 | 1330.9 | 1 | 762 | 761 |
13 | XP_010547469 | 887 | 1321.6 | 1321.4 | 1 | 762 | 761 |
14 | KAA8549067 | 880 | 1318.5 | 1318.3 | 1 | 762 | 761 |
15 | KAF9593489 | 867 | 1316.0 | 1315.8 | 1 | 762 | 761 |
16 | GBHQ01019601.1_F_862758 | 891 | 1315.1 | 1314.9 | 1 | 762 | 761 |
17 | XP_011079534 | 856 | 1314.0 | 1313.8 | 1 | 762 | 761 |
18 | GFZ19314 | 855 | 1310.7 | 1310.6 | 1 | 762 | 761 |
19 | KAG8389576 | 864 | 1309.2 | 1309.0 | 1 | 761 | 760 |
20 | XP_026436484 | 866 | 1309.0 | 1308.8 | 1 | 762 | 761 |
21 | KAG9457836 | 837 | 1308.2 | 1308.0 | 1 | 762 | 761 |
22 | KAF7120881 | 866 | 1308.0 | 1307.8 | 1 | 762 | 761 |
23 | KAF6170924 | 853 | 1306.3 | 1306.1 | 1 | 761 | 760 |
24 | GCZN01065873.1_F_1832885 | 901 | 1305.6 | 1305.4 | 1 | 762 | 761 |
25 | GCKF01036955.1_F_2642786 | 841 | 1303.7 | 831.4 | 1 | 470 | 469 |
26 | GCKF01036955.1_F_2642786 | 841 | 1303.7 | 476.2 | 518 | 762 | 244 |
27 | XP_027118604 | 866 | 1302.9 | 1302.8 | 1 | 762 | 761 |
28 | XP_006841446 | 857 | 1302.8 | 1302.6 | 1 | 762 | 761 |
29 | CAA3012856 | 850 | 1302.2 | 1302.0 | 1 | 762 | 761 |
30 | GCHU01013499.1_F_2622784 | 841 | 1301.7 | 831.0 | 1 | 470 | 469 |
⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ | ⋮ |
Family | Clade | |
---|---|---|
String | String | |
1 | Haematococcaceae | Green Algae |
2 | Chlamydomonadaceae | Green Algae |
3 | Ulvaceae | Green Algae |
4 | Chlorodendraceae | Green Algae |
5 | Juglandaceae | Core Eudicots/Rosids |
6 | Dunaliellaceae | Green Algae |
7 | Aphanochaetaceae | Green Algae |
8 | Nephroselmidaceae | Green Algae |
9 | Volvocaceae | Green Algae |
10 | Hydrodictyaceae | Green Algae |
11 | Goniaceae | Green Algae |
12 | Oocystaceae | Green Algae |
13 | Thelypteridaceae | Leptosporangiate Monilophytes |
14 | Agapanthaceae | Monocots |
15 | Pleurastraceae | Green Algae |
16 | Actinidiaceae | Core Eudicots/Asterids |
17 | Hymenophyllaceae | Leptosporangiate Monilophytes |
18 | Carteriaceae | Green Algae |
19 | Monocleaceae | Liverworts |
20 | Pyramimonadaceae | Green Algae |
21 | Cyrillaceae | Core Eudicots/Asterids |