Have list of biomineralization genes from coral literature (e.g., Takeuchi et al. 2016, Ramos-Silva et al. 2013)
| Accession / GeneID | Blasted protein in Stylophora | Definition | Reference |
|---|---|---|---|
| AAD11470.1 | XP_022803851.1 | L-type calcium channel alpha-1 subunit | Zoccola et al., 1999 |
| AAR13013.1 | XP_022785723.1 | plasma membrane calcium ATPase | Zoccola et al., 2004 |
| ACE95141.1 | XP_022799914.1 | carbonic anhydrase | Moya et al., 2008 |
| AGE35225.2 | XP_022785805.1 | CARP1 | Mass et al., 2013 |
| AGE35226.1 | XP_022794102.1 | CARP3 | Mass et al., 2013 |
| AGG36361.1 | XP_022784808.1 | Protoacadherin (PC4) | Drake et al., 2013 |
| AJQ31790.1 | XP_022788307.1 | solute carrier family 4 member gamma | Zoccola et al., 2015 |
| aug_v2a.00002.t1 | XP_022808048.1, XP_022808045.1, XP_022790310.1 | EP-like 2 | Takeuchi et al., 2016 |
| aug_v2a.01440.t1 (aug_v2a.01441.t1) | XP_022780690.1 | Adi-SAARP2 | Takeuchi et al., 2016 |
| aug_v2a.02830 | XP_022782704.1, XP_022782703.1 | PKD1-related protein | Takeuchi et al., 2016 |
| aug_v2a.02830.t1 | XP_022782704.1, XP_022782703.1 | PKD1-related protein | Takeuchi et al., 2016 |
| aug_v2a.05945.t1 | XP_022783430.1 | TSP-1 and VWA domain-containing | Takeuchi et al., 2016 |
| aug_v2a.06122.t1 | XP_022804012.1 | EGF & laminin G domain protein | Takeuchi et al., 2016 |
| aug_v2a.06123.t1 | XP_022804012.1 | EGF & laminin G domain protein | Takeuchi et al., 2016 |
| aug_v2a.06327.t1 | XP_022781839.1, XP_022781915.1 | SAARP3 | Takeuchi et al., 2016 |
| aug_v2a.07627.t1 | XP_022806326.1 | Zona pellucida domain protein | Takeuchi et al., 2016 |
| aug_v2a.09809.t1 | XP_022801334.1 | Mucin4-like protein | Takeuchi et al., 2016 |
| aug_v2a.09968.t1 | XP_022794736.1 | MAM & LDLr domain protein | Takeuchi et al., 2016 |
| aug_v2a.09969.t1 | XP_022794736.1 | MAM & LDLr domain protein | Takeuchi et al., 2016 |
| aug_v2a.11068.t1 | XP_022782398.1 | SAARP1 | Takeuchi et al., 2016 |
| aug_v2a.15064.t1 | XP_022808152.1 | Cysteine-rich | Takeuchi et al., 2016 |
| aug_v2a.15065.t1 | XP_022794122.1, XP_022794121.1 | galaxin2 | Takeuchi et al., 2016 |
| aug_v2a.15580.t1 | XP_022804012.1 | Laminin G domain protein | Takeuchi et al., 2016 |
| aug_v2a.18631.t1 | XP_022794122.1, XP_022794121.1 | galaxin | Takeuchi et al., 2016 |
| aug_v2a.19518.t1 | XP_022784808.1 | Protocadherin-like | Takeuchi et al., 2016 |
| aug_v2a.22918.t1 | XP_022808048.1, XP_022808045.1, XP_022790310.1 | EP-like1 | Takeuchi et al., 2016 |
| aug_v2a.24015.t1 | XP_022788227.1 | Hephaestin-like protein | Takeuchi et al., 2016 |
| aug_v2a.24512.t1 | XP_022804012.1 | EGF & laminin G domain protein | Takeuchi et al., 2016 |
| EU532164.1 | XP_022799914.1 | carbonic anhydrase 2 | Bertucci et al., 2011 |
| Gene:g29033.t1 | XP_022799914.1 | Carbonic Anhydrase (STPCA2-1) | Mummadisetti et al., 2021 |
| Gene:g3745.t1 | XP_022782398.1 | CARP4 | Mummadisetti et al., 2021 |
| Gene:10186 | XP_022784808.1 | Protocadherin (PC2) | Mummadisetti et al., 2021 |
| Gene:g10186 | XP_022782398.1 | CARP4 | Mummadisetti et al., 2021 |
| Gene:g10187 | XP_022784808.1 | Protocadherin (PC3) | Mummadisetti et al., 2021 |
| Gene:g10188 | XP_022784808.1 | Protocadherin (PC3) | Mummadisetti et al., 2021 |
| Gene:g11190 | XP_022783323.1 | USOMP12 | Mummadisetti et al., 2021 |
| Gene:g13552 | XP_022781839.1 | Acidic SOMP (p27) | Mummadisetti et al., 2021 |
| Gene:g14733 | XP_022782398.1 | CARP4 | Mummadisetti et al., 2021 |
| Gene:g1484 | XP_022785805.1 | CARP1 | Mummadisetti et al., 2021 |
| Gene:g15294.t1 | XP_022779720.1 | Vitellogenin | Mummadisetti et al., 2021 |
| Gene:g15955 | XP_022794736.1 | MAM LDL-2 | Mummadisetti et al., 2021 |
| Gene:g2115 | XP_022784808.1 | Cadherin | Mummadisetti et al., 2021 |
| Gene:g2116 | XP_022784808.1 | Protocadherin (PC1) | Mummadisetti et al., 2021 |
| Gene:g22569 | XP_022810031.1 | Fibronectin | Mummadisetti et al., 2021 |
| Gene:g24177 | XP_022798258.1 | Protocadherin (PC5) | Mummadisetti et al., 2021 |
| Gene:g27814 | XP_022801359.1 | carbonic anhydrase (STPCA2-2) | Mummadisetti et al., 2021 |
| Gene:g2829 | XP_022783414.1, XP_022783413.1 | Thrombospondin | Mummadisetti et al., 2021 |
| Gene:g2829.t1 | XP_022783415.1 | Coadhesin | Mummadisetti et al., 2021 |
| Gene:g29034.t1 | XP_022799914.1 | Carbonic Anhydrase | Mummadisetti et al., 2021 |
| Gene:g30 | XP_022784808.1 | Protoacadherin (PC4) | Mummadisetti et al., 2021 |
| Gene:g30385.t1 | XP_022780049.1 | USOMPS13 | Mummadisetti et al., 2021 |
| Gene:g34749 | XP_022804012.1 | EGF & LamininG-Like | Mummadisetti et al., 2021 |
| Gene:g37058 | XP_022804608.1 | Fibronectin-2 | Mummadisetti et al., 2021 |
| Gene:g38128 | XP_022783430.1 | α-Collagen | Mummadisetti et al., 2021 |
| Gene:g38881 | XP_022790556.1, XP_022790555.1 | USOMP14 | Mummadisetti et al., 2021 |
| Gene:g39770 | XP_022795871.1 | Kielin-Like | Mummadisetti et al., 2021 |
| Gene:g5735.t1 | XP_022799127.1 | Tolloid-Like | Mummadisetti et al., 2021 |
| Gene:g7086 | XP_022804012.1 | EGF LamG1 | Mummadisetti et al., 2021 |
| Gene:g8396 | XP_022803859.1 | CARP6-partial | Mummadisetti et al., 2021 |
| Gene:g907 | XP_022806326.1 | Zona Pellucida | Mummadisetti et al., 2021 |
| Gene:g9094 | XP_022795459.1, XP_022777933.1 | Actin | Mummadisetti et al., 2021 |
| HM163215 | XP_029187982.1 | Acropora millepora galaxin | Reyes-Bermudez et al., 2009 |
| JN631095.1 | XP_029195765.1 | hypothetical protein p251_4 | Hayward et al., 2011 |
| JR971508.1 | XP_022793420.1, XP_022793422.1 | USOMP6 | Ramos-Silva et al., 2013 |
| JR972076.1 | XP_022781839.1, XP_022781915.1 | Acidic SOMP | Ramos-Silva et al., 2013 |
| JR973117.1 | XP_022808048.1, XP_022808045.1 | USOMP-5 | Ramos-Silva et al., 2013 |
| JR976690.1 | XP_022794122.1, XP_022794121.1 | Galaxin 2 | Ramos-Silva et al., 2013 |
| JR980881.1 | XP_022804012.1 | EGF & laminin G protein | Ramos-Silva et al., 2013 |
| JR982706.1 | XP_022808152.1 | USOMP-2 | Ramos-Silva et al., 2013 |
| JR986059.1 | XP_022782738.1 | Cephalotoxin-like | Ramos-Silva et al., 2013 |
| JR991083.1 | XP_022779335.1 | Collagen α-1 chain | Ramos-Silva et al., 2013 |
| JR991407.1 | XP_022780690.1 | SAARP2 | Ramos-Silva et al., 2013 |
| JR994474.1 | XP_022794736.1 | MAM & LDL-receptor protein 2 | Ramos-Silva et al., 2013 |
| JR997000.1 | XP_022807628.1, XP_022807627.1 | USOMP-3 | Ramos-Silva et al., 2013 |
| JR998014.1 | XP_022799897.1, XP_022801331.1 | Putative carbonic anhydrase | Ramos-Silva et al., 2013 |
| JR998260.1 | XP_022803212.1 | USOMP7 | Ramos-Silva et al., 2013 |
| JT001945.1 | XP_022782398.1 | SAARP1 | Ramos-Silva et al., 2013 |
| JT004498.1 | XP_022780690.1 | USOMP-4 | Ramos-Silva et al., 2013 |
| JT011118.1 | XP_022794736.1 | MAM LDL receptor protein 1 | Ramos-Silva et al., 2013 |
| JT014391.1 | XP_022797021.1 | USOMP-8 | Ramos-Silva et al., 2013 |
| JT016638.1 | XP_022783430.1 | Coadhesin | Ramos-Silva et al., 2013 |
| MG182344.1 | XP_022792788.1 | Acropora yongei Na+/Ca2+ exchanger | Barron et al., 2018 |
| MG182345.1 | XP_022784107.1 | Acropora yongei Na+/Ca2+ exchanger | Barron et al., 2018 |
| P12_g2385 | XP_022796981.1 | hypothetical protein | Drake et al., 2013 |
| P13_g6918 | XP_022803207.1 | Sushi domain-containing | Drake et al., 2013 |
| P14_g9951 | XP_022783415.1 | collagen-like protein | Drake et al., 2013 |
| P15_g1532 | XP_022780640.1, XP_022783414.1 | CARP9 | Drake et al., 2013 |
| P16_g11702 | XP_022780049.1 | hypothetical protein | Drake et al., 2013 |
| P18_g810 | XP_022783430.1 | collagen-like protein | Drake et al., 2013 |
| P19_g20041 | XP_022804012.1 | Contactin-associated protein | Drake et al., 2013 |
| P2_g11187 | XP_022782364.1 | CARP8 | Drake et al., 2013 |
| P20_g6066 | XP_022794736.1 | MAM domain anchor protein | Drake et al., 2013 |
| P21_g18277 | XP_022806326.1 | Zona pellucida | Drake et al., 2013 |
| P22_g19762 | XP_022785540.1 | hypothetical protein | Drake et al., 2013 |
| P23_g1057 | XP_022808083.1, XP_022808082.1 | Protocadherin | Drake et al., 2013 |
| P24_g15888 | XP_022779720.1 | vitellogenin-like protein | Drake et al., 2013 |
| P26_g1441 | XP_022794920.1 | vitellogenin-like protein | Drake et al., 2013 |
| P27_g18472 | XP_022781915.1 | Integrin-alpha | Drake et al., 2013 |
| P28_g11651 | XP_022793421.1 | Late embryogenesis protein | Drake et al., 2013 |
| P3_g12510 | XP_022783415.1 | Thrombospondin | Drake et al., 2013 |
| P31_g20420 | XP_022804012.1 | Neurexin | Drake et al., 2013 |
| P32_g5540 | XP_022795871.1 | Kielin/chordin-like | Drake et al., 2013 |
| P33_g8985 | XP_022781364.1 | Flagellar associated protein | Drake et al., 2013 |
| P34_g1714 | XP_022794736.1 | MAM/LDL receptor domain protein | Drake et al., 2013 |
| P36_g13890 | XP_022794736.1 | Zonadhesion-like precursor | Drake et al., 2013 |
| P4_g9861 | XP_022797264.1 | Viral inclusion protein | Drake et al., 2013 |
| P5_g11674 | XP_022783415.1 | Hemicentin | Drake et al., 2013 |
| P8_g9654 | XP_022786917.1, XP_022786918.1 | Major yolk protein | Drake et al., 2013 |
| P9_g10811; P1_g11108; P10_g11107 | XP_022784808.1 | Protocadherin fat-like | Drake et al., 2013 |
| PFX13778.1 | XP_022808646.1 | Sacsin | Peled et al., 2020 |
| PFX14205.1 | XP_022808089.1 | Ret receptor kinase (partial) | Peled et al., 2020 |
| PFX15740.1 | XP_022806058.1 | Protein FAM208A | Peled et al., 2020 |
| PFX16398.1 | XP_022805070.1 | hypothetical protein | Peled et al., 2020 |
| PFX18785.1 | XP_022801334.1, XP_022801335.1 | Mucin-4 | Peled et al., 2020 |
| PFX26597.1 | XP_022788977.1 | Complement C3 | Peled et al., 2020 |
| PFX26751.1 | XP_022788730.1 | Transmembrane protease serine 9 | Peled et al., 2020 |
| PFX27832.1 | XP_022786864.1 | PARP11 | Peled et al., 2020 |
| PFX30903.1 | XP_022781839.1 | hypothetical protein | Peled et al., 2020 |
| XP_022778254.1 | XP_022778254.1 | uncharacterized protein LOC111319781 | Peled et al., 2020 |
| XP_022778283.1 | XP_022778283.1 | uncharacterized protein LOC111319816 | Peled et al., 2020 |
| XP_022779720.1 | XP_022779720.1 | vitellogenin-like | Peled et al., 2020 |
| XP_022780303.1 | XP_022780303.1 | uncharacterized protein LOC111321626 | Peled et al., 2020 |
| XP_022780690.1 | XP_022780690.1 | CARP5 | Peled et al., 2020 |
| XP_022780694.1 | XP_022780694.1 | CUB & peptidase domain protein | Peled et al., 2020 |
| XP_022781731.1 | XP_022781731.1 | sulfate anion transporter-like 2C | Zoccola et al., 2015 |
| XP_022782398.1 | XP_022782398.1 | CARP4 | Peled et al., 2020 |
| XP_022783031.1 | XP_022783031.1 | sodium bicarbonate transporter-like 11 | Zoccola et al., 2015 |
| XP_022783044.1 | XP_022783044.1 | uncharacterized protein LOC111323869 | Peled et al., 2020 |
| XP_022783323.1 | XP_022783323.1 | VHS3-like | Peled et al., 2020 |
| XP_022783415.1 | XP_022783415.1 | coadhesin-like isoform X3 | Peled et al., 2020 |
| XP_022783952.1 | XP_022783952.1 | collagenase 3-like | Peled et al., 2020 |
| XP_022784623.1 | XP_022784623.1 | sperm-associated cation channel | Peled et al., 2020 |
| XP_022786582.1 | XP_022786582.1 | synapsin-2-like isoform X2 | Peled et al., 2020 |
| XP_022786918.1 | XP_022786918.1 | major yolk protein-like X2 | Peled et al., 2020 |
| XP_022788227.1 | XP_022788227.1 | hephaestin-like protein | Peled et al., 2020 |
| XP_022788270.1 | XP_022788270.1 | band 3 anion transport protein-like | Zoccola et al., 2015 |
| XP_022788730.1 | XP_022788730.1 | elastase-like peptidase | Peled et al., 2020 |
| XP_022789591.1 | XP_022789591.1 | endothelin-converting enzyme 1-like X2 | Peled et al., 2020 |
| XP_022789932.1 | XP_022789932.1 | MAGUK p55 subfamily member 7-like | Peled et al., 2020 |
| XP_022790441.1 | XP_022790441.1 | PHD finger protein 21A-like | Peled et al., 2020 |
| XP_022791567.1 | XP_022791567.1 | anion exchange protein 2-like | Zoccola et al., 2015 |
| XP_022792212.1 | XP_022792212.1 | ras-like protein 3 | Peled et al., 2020 |
| XP_022794122.1 | XP_022794122.1 | galaxin-like isoform X2 | Peled et al., 2020 |
| XP_022794351.1 | XP_022794351.1 | ependymin-related protein | Peled et al., 2020 |
| XP_022794736.1 | XP_022794736.1 | MAM & LDL receptor protein 2-like | Peled et al., 2020 |
| XP_022796981.1 | XP_022796981.1 | skeletal organic matrix protein 8-like | Peled et al., 2020 |
| XP_022796982.1 | XP_022796982.1 | uncharacterized protein LOC111335364 | Peled et al., 2020 |
| XP_022798902.1 | XP_022798902.1 | LDL receptor-related protein 8-like | Peled et al., 2020 |
| XP_022799089.1 | XP_022799089.1 | CUB domain protein isoform X2 | Peled et al., 2020 |
| XP_022799541.1 | XP_022799541.1 | uncharacterized protein LOC111337489 | Peled et al., 2020 |
| XP_022800320.1 | XP_022800320.1 | sulfate anion transporter 1-like X1 | Zoccola et al., 2015 |
| XP_022800329.1 | XP_022800329.1 | sulfate anion transporter 1-like X2 | Zoccola et al., 2015 |
| XP_022800339.1 | XP_022800339.1 | sulfate anion transporter 1-like X1 | Zoccola et al., 2015 |
| XP_022801463.1 | XP_022801463.1 | bicarbonate cotransporter 3-like X2 | Zoccola et al., 2015 |
| XP_022803524.1 | XP_022803524.1 | digestive cysteine proteinase 1-like | Peled et al., 2020 |
| XP_022803808.1 | XP_022803808.1 | tumor suppressor DMBT1-like | Peled et al., 2020 |
| XP_022803872.1 | XP_022803872.1 | spore wall protein 2-like X3 | Peled et al., 2020 |
| XP_022803894.1 | XP_022803894.1 | uncharacterized protein LOC111341206 | Peled et al., 2020 |
| XP_022804012.1 | XP_022804012.1 | EGF & laminin G domain protein | Peled et al., 2020 |
| XP_022804785.1 | XP_022804785.1 | thioredoxin reductase 1-like | Peled et al., 2020 |
| XP_022805470.1 | XP_022805470.1 | uncharacterized protein LOC111342641 | Peled et al., 2020 |
| XP_022806326.1 | XP_022806326.1 | ZP domain protein | Peled et al., 2020 |
| XP_022806664.1 | XP_022806664.1 | protein lingerer-like | Peled et al., 2020 |
| XP_022806928.1 | XP_022806928.1 | SLIT-ROBO RhoGAP1-like | Peled et al., 2020 |
| XP_022807143.1 | XP_022807143.1 | condensin-2 subunit D3-like | Peled et al., 2020 |
| XP_022807256.1 | XP_022807256.1 | uncharacterized protein LOC111344300 | Peled et al., 2020 |
| XP_022807807.1 | XP_022807807.1 | uncharacterized protein LOC111344812 | Peled et al., 2020 |
| XP_022808163.1 | XP_022808163.1 | uncharacterized protein LOC111345150 | Peled et al., 2020 |
| XP_022808576.1 | XP_022808576.1 | LOC111345553 isoform X2 | Peled et al., 2020 |
| XP_022809269.1 | XP_022809269.1 | microtubule-associated tumor suppressor 1-like X1 | Peled et al., 2020 |
| XP_022809270.1 | XP_022809270.1 | microtubule-associated tumor suppressor 1-like X2 | Peled et al., 2020 |
| XP_022810585.1 | XP_022810585.1 | vWF D + EGF domain protein (partial) | Peled et al., 2020 |
seqkit grep -f ../data/biomin-ids.txt ../data/GCF_002571385.2_Stylophora_pistillata_v1.1_protein.faa > ../output/31-biomin-pathway/Stylo-biomin.fastablastp \
-query ../output/11.3-ortholog-annotation/representative_sequences.faa \
-db ../output/31-biomin-pathway/Stylo-biomin-db \
-out ../output/31-biomin-pathway/OG-repseq_Stylo-biomin-results.tsv \
-outfmt "6 qseqid sseqid evalue bitscore" \
-evalue 1e-20 \
-max_target_seqs 1 \
-max_hsps 1 \
-num_threads 10head ../output/31-biomin-pathway/OG-repseq_Stylo-biomin-results.tsvFUN_000236-T1 XP_022780303.1 6.14e-24 102
FUN_000857-T1 XP_022795459.1 1.39e-159 447
FUN_000867-T1 XP_022780694.1 1.60e-34 125
FUN_001009-T1 XP_022789591.1 7.04e-107 338
FUN_001088-T1 XP_022783044.1 3.90e-35 130
FUN_001089-T1 XP_022783044.1 2.17e-23 93.2
FUN_001101-T1 XP_022783044.1 1.22e-31 118
FUN_001107-T1 XP_022795459.1 9.45e-59 190
FUN_001118-T1 XP_022801359.1 1.33e-35 124
FUN_001185-T1 XP_022798902.1 0.0 870head ../output/11.3-ortholog-annotation/gene_to_ortholog_mapping.csvgene_id,species,group_id,type,conservation_level
FUN_000185-T1,Apul,OG_00001,three_way,medium
Peve_00037402,Peve,OG_00001,three_way,medium
Pocillopora_meandrina_HIv1___RNAseq.g28886.t1,Ptua,OG_00001,three_way,medium
FUN_000189-T1,Apul,OG_00002,three_way,medium
Peve_00038462,Peve,OG_00002,three_way,medium
Pocillopora_meandrina_HIv1___RNAseq.g28888.t3,Ptua,OG_00002,three_way,medium
FUN_000190-T1,Apul,OG_00003,three_way,low
Peve_00038463,Peve,OG_00003,three_way,low
Pocillopora_meandrina_HIv1___RNAseq.g28889.t1,Ptua,OG_00003,three_way,lowlibrary(dplyr)
library(readr)
# Paths
blast_file <- "../output/31-biomin-pathway/OG-repseq_Stylo-biomin-results.tsv"
mapping_file <- "../output/11.3-ortholog-annotation/gene_to_ortholog_mapping.csv"
# Read BLAST results
blast <- read_tsv(
blast_file,
col_names = c("gene_id", "hit", "evalue", "score")
)
# Read ortholog mapping
mapping <- read_csv(mapping_file)
# Join to add group_id to each gene in blast results
annotated <- blast %>%
left_join(mapping %>% select(gene_id, group_id), by = "gene_id")
# Write out CSV
write_csv(annotated, "../output/31-biomin-pathway/OG-repseq_Stylo-biomin.csv")
# View result
annotated
Matches in Barnacle
library(tidyverse)
# 1. Load the Stylo-biomin group_id list
stylo_file <- "../output/31-biomin-pathway/OG-repseq_Stylo-biomin.csv"
stylo_groups <- read_csv(stylo_file) %>%
pull(group_id) %>%
unique()
# 2. Get all *_top100.csv files
path_top100 <- "../output/22-Visualizing-Rank-outs"
top100_files <- list.files(
path_top100,
pattern = "*_top100.csv",
full.names = TRUE
)
# 3. For each file, find matching group IDs in column 1
results <- map_df(top100_files, function(f) {
df <- read_csv(f, col_names = FALSE)
# assume the first column has the group_ids
col1_ids <- df[[1]] %>% unique()
matches <- intersect(stylo_groups, col1_ids)
tibble(
file = basename(f),
matched_group_id = matches
)
})
# Show results
results
# 4. Write out summary file
write_csv(
results,
"../output/31-biomin-pathway/Stylo-biomin_matches_in_top100.csv"
)library(tidyverse)
# Read the file: it has two columns (file, group_id)
res <- read_csv("../output/31-biomin-pathway/Stylo-biomin_matches_in_top100.csv",
col_names = c("file", "group_id"))
# Count occurrences of each file (column 1)
file_counts <- res %>%
count(file, name = "n_occurrences") %>%
arrange(desc(n_occurrences))
file_counts
WGCNA module enrichment
library(tidyverse)
# 1. Load biomin group IDs
biomin_groups <- read_csv("../output/31-biomin-pathway/OG-repseq_Stylo-biomin.csv") %>%
pull(group_id) %>%
unique()
n_biomin <- length(biomin_groups) # total number of biomin groups
# 2. Load module assignments (must contain group_id and module_label)
assignments <- read_csv(
"~/GitHub/timeseries_molecular/M-multi-species/output/18-ortholog-wgcna/gene_module_assignments.csv"
)
# 3. Mark biomin matches
assignments2 <- assignments %>%
mutate(is_biomin = group_id %in% biomin_groups)
# 4. Summarize by module_label
module_summary <- assignments2 %>%
group_by(module_label) %>%
summarise(
n_group_ids_in_module = n_distinct(group_id),
n_biomin_in_module = sum(is_biomin),
# percent of BIOMIN groups captured by this module
pct_of_all_biomin = (n_biomin_in_module / n_biomin) * 100,
# percent of module that is biomin
pct_of_module_that_is_biomin = (n_biomin_in_module / n_group_ids_in_module) * 100
) %>%
arrange(desc(pct_of_all_biomin))
module_summary