Comments (3)
Here is the data:
gff_subs <- structure(list(seq_id = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L), .Label = c("LBN7-1_scf1",
"LMX7-1_scf1", "LMX7-1_scf2"), class = "factor"), source = structure(c(4L,
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L,
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L,
4L, 4L), .Label = c("cmsearch", "GeneMarkS-2+", "Local", "Protein Homology",
"tRNAscan-SE"), class = "factor"), type = structure(c(1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L), .Label = c("CDS", "exon", "gene", "pseudogene", "pseudogenic_tRNA",
"region", "riboswitch", "RNase_P_RNA", "rRNA", "SRP_RNA", "tmRNA",
"tRNA"), class = "factor"), start = c(0L, 871L, 2092L, 3598L,
4028L, 4649L, 6013L, 6689L, 7387L, 9567L, 10918L, 12472L, 13217L,
14839L, 15972L, 17521L, 18636L, 19642L, 21049L, 22577L, 24119L,
24806L, 0L, 758L, 2145L, 3548L, 4852L, 7184L, 7734L, 8477L, 9819L,
10422L, 11074L, 12472L, 13565L), end = c(866L, 1947L, 3348L,
3987L, 4591L, 5851L, 6681L, 7231L, 9564L, 10877L, 12299L, 13095L,
14461L, 15936L, 17483L, 18582L, 19598L, 20595L, 22431L, 23773L,
24574L, 25141L, 335L, 1972L, 3527L, 4849L, 7029L, 7726L, 8402L,
9763L, 10382L, 10811L, 12330L, 13527L, 14431L), score = c(NA_real_,
NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_,
NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_,
NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_,
NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_,
NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_),
strand = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L,
2L, 2L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 2L,
1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L), .Label = c("-",
"+"), class = "factor"), phase = structure(c(1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L), .Label = c("0", "1", "2"), class = "factor"), ID = c("cds-LBN7-1.2_001106",
"cds-LBN7-1.2_001107", "cds-LBN7-1.2_001108", "cds-LBN7-1.2_001109",
"cds-LBN7-1.2_001110", "cds-LBN7-1.2_001111", "cds-LBN7-1.2_001112",
"cds-LBN7-1.2_001113", "cds-LBN7-1.2_001114", "cds-LBN7-1.2_001115",
"cds-LBN7-1.2_001116", "cds-LBN7-1.2_001117", "cds-LBN7-1.2_001118",
"cds-LBN7-1.2_001119", "cds-LBN7-1.2_001120", "cds-LBN7-1.2_001121",
"cds-LBN7-1.2_001122", "cds-LBN7-1.2_001123", "cds-LBN7-1.2_001124",
"cds-LBN7-1.2_001125", "cds-LBN7-1.2_001126", "cds-LBN7-1.2_001127",
"cds-LMX7-1.2_002664", "cds-LMX7-1.2_002665", "cds-LMX7-1.2_002666",
"cds-LMX7-1.2_002667", "cds-LMX7-1.2_002668", "cds-LMX7-1.2_002669",
"cds-LMX7-1.2_002670", "cds-LMX7-1.2_002671", "cds-LMX7-1.2_002672",
"cds-LMX7-1.2_002673", "cds-LMX7-1.2_002674", "cds-LMX7-1.2_002675",
"cds-LMX7-1.2_002676"), Dbxref = c(NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_), Name = c("extdb:LBN7-1.2_001106", "extdb:LBN7-1.2_001107",
"extdb:LBN7-1.2_001108", "extdb:LBN7-1.2_001109", "extdb:LBN7-1.2_001110",
"extdb:LBN7-1.2_001111", "extdb:LBN7-1.2_001112", "extdb:LBN7-1.2_001113",
"extdb:LBN7-1.2_001114", "extdb:LBN7-1.2_001115", NA, "extdb:LBN7-1.2_001117",
"extdb:LBN7-1.2_001118", "extdb:LBN7-1.2_001119", "extdb:LBN7-1.2_001120",
"extdb:LBN7-1.2_001121", "extdb:LBN7-1.2_001122", "extdb:LBN7-1.2_001123",
"extdb:LBN7-1.2_001124", "extdb:LBN7-1.2_001125", "extdb:LBN7-1.2_001126",
"extdb:LBN7-1.2_001127", "extdb:LMX7-1.2_002664", "extdb:LMX7-1.2_002665",
"extdb:LMX7-1.2_002666", "extdb:LMX7-1.2_002667", "extdb:LMX7-1.2_002668",
"extdb:LMX7-1.2_002669", "extdb:LMX7-1.2_002670", "extdb:LMX7-1.2_002671",
"extdb:LMX7-1.2_002672", "extdb:LMX7-1.2_002673", "extdb:LMX7-1.2_002674",
"extdb:LMX7-1.2_002675", "extdb:LMX7-1.2_002676"), gbkey = c("CDS",
"CDS", "CDS", "CDS", "CDS", "CDS", "CDS", "CDS", "CDS", "CDS",
"CDS", "CDS", "CDS", "CDS", "CDS", "CDS", "CDS", "CDS", "CDS",
"CDS", "CDS", "CDS", "CDS", "CDS", "CDS", "CDS", "CDS", "CDS",
"CDS", "CDS", "CDS", "CDS", "CDS", "CDS", "CDS"), genome = c(NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_), mol_type = c(NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_), strain = c(NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_), gene_biotype = c(NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_), feat_id = c("LBN7-1.2_001106",
"LBN7-1.2_001107", "LBN7-1.2_001108", "LBN7-1.2_001109",
"LBN7-1.2_001110", "LBN7-1.2_001111", "LBN7-1.2_001112",
"LBN7-1.2_001113", "LBN7-1.2_001114", "LBN7-1.2_001115",
"LBN7-1.2_001116", "LBN7-1.2_001117", "LBN7-1.2_001118",
"LBN7-1.2_001119", "LBN7-1.2_001120", "LBN7-1.2_001121",
"LBN7-1.2_001122", "LBN7-1.2_001123", "LBN7-1.2_001124",
"LBN7-1.2_001125", "LBN7-1.2_001126", "LBN7-1.2_001127",
"LMX7-1.2_002664", "LMX7-1.2_002665", "LMX7-1.2_002666",
"LMX7-1.2_002667", "LMX7-1.2_002668", "LMX7-1.2_002669",
"LMX7-1.2_002670", "LMX7-1.2_002671", "LMX7-1.2_002672",
"LMX7-1.2_002673", "LMX7-1.2_002674", "LMX7-1.2_002675",
"LMX7-1.2_002676"), partial = c(NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_), start_range = c(NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_), Parent = c("gene-LBN7-1.2_001106", "gene-LBN7-1.2_001107",
"gene-LBN7-1.2_001108", "gene-LBN7-1.2_001109", "gene-LBN7-1.2_001110",
"gene-LBN7-1.2_001111", "gene-LBN7-1.2_001112", "gene-LBN7-1.2_001113",
"gene-LBN7-1.2_001114", "gene-LBN7-1.2_001115", "gene-LBN7-1.2_001116",
"gene-LBN7-1.2_001117", "gene-LBN7-1.2_001118", "gene-LBN7-1.2_001119",
"gene-LBN7-1.2_001120", "gene-LBN7-1.2_001121", "gene-LBN7-1.2_001122",
"gene-LBN7-1.2_001123", "gene-LBN7-1.2_001124", "gene-LBN7-1.2_001125",
"gene-LBN7-1.2_001126", "gene-LBN7-1.2_001127", "gene-LMX7-1.2_002664",
"gene-LMX7-1.2_002665", "gene-LMX7-1.2_002666", "gene-LMX7-1.2_002667",
"gene-LMX7-1.2_002668", "gene-LMX7-1.2_002669", "gene-LMX7-1.2_002670",
"gene-LMX7-1.2_002671", "gene-LMX7-1.2_002672", "gene-LMX7-1.2_002673",
"gene-LMX7-1.2_002674", "gene-LMX7-1.2_002675", "gene-LMX7-1.2_002676"
), inference = c("COORDINATES: similar to AA sequence:RefSeq:WP_019180136.1",
"COORDINATES: protein motif:HMM:NF012742.2", "COORDINATES: similar to AA sequence:RefSeq:WP_007542666.1",
"COORDINATES: protein motif:HMM:NF013228.2", "COORDINATES: similar to AA sequence:RefSeq:WP_013585224.1",
"COORDINATES: protein motif:HMM:NF019640.2", "COORDINATES: similar to AA sequence:RefSeq:WP_019482283.1",
"COORDINATES: similar to AA sequence:RefSeq:WP_019482282.1",
"COORDINATES: similar to AA sequence:RefSeq:WP_019180140.1",
"COORDINATES: similar to AA sequence:RefSeq:WP_019482280.1",
"COORDINATES: protein motif:HMM:NF012398.2", "COORDINATES: similar to AA sequence:RefSeq:WP_012865089.1",
"COORDINATES: protein motif:HMM:NF019640.2", "COORDINATES: protein motif:HMM:NF024799.2",
"COORDINATES: protein motif:HMM:NF012235.2", "COORDINATES: protein motif:HMM:NF014684.2",
"COORDINATES: protein motif:HMM:NF019474.2", "COORDINATES: similar to AA sequence:RefSeq:WP_010156141.1",
"COORDINATES: similar to AA sequence:RefSeq:WP_020145555.1",
"COORDINATES: protein motif:HMM:NF019640.2", "COORDINATES: protein motif:HMM:NF019498.2",
"COORDINATES: protein motif:HMM:NF013228.2", "COORDINATES: protein motif:HMM:NF013228.2",
"COORDINATES: protein motif:HMM:NF019640.2", "COORDINATES: similar to AA sequence:RefSeq:WP_020075570.1",
"COORDINATES: similar to AA sequence:RefSeq:WP_019617933.1",
"COORDINATES: similar to AA sequence:RefSeq:WP_019180140.1",
"COORDINATES: similar to AA sequence:RefSeq:WP_019482282.1",
"COORDINATES: similar to AA sequence:RefSeq:WP_019482283.1",
"COORDINATES: protein motif:HMM:NF019640.2", "COORDINATES: similar to AA sequence:RefSeq:WP_017197468.1",
"COORDINATES: protein motif:HMM:NF013228.2", "COORDINATES: similar to AA sequence:RefSeq:WP_007542666.1",
"COORDINATES: protein motif:HMM:NF012742.2", "COORDINATES: similar to AA sequence:RefSeq:WP_019180136.1"
), product = c("NAD(P)-dependent oxidoreductase", "LacI family transcriptional regulator",
"Xaa-Pro peptidase family protein", "RidA family protein",
"flavin reductase family protein", "acyl-CoA dehydrogenase family protein",
"GntR family transcriptional regulator", "VOC family protein",
"thiamine pyrophosphate-dependent enzyme", "2-oxo acid dehydrogenase subunit E2",
"aldehyde dehydrogenase family protein", "NADPH-dependent F420 reductase",
"acyl-CoA dehydrogenase family protein", "sugar ABC transporter substrate-binding protein",
"sugar ABC transporter ATP-binding protein", "ABC transporter permease",
"alpha/beta hydrolase", "DMT family transporter", "Xaa-Pro peptidase family protein",
"acyl-CoA dehydrogenase family protein", "cupin domain-containing protein",
"RidA family protein", "RidA family protein", "acyl-CoA dehydrogenase family protein",
"aldehyde dehydrogenase family protein", "2-oxo acid dehydrogenase subunit E2",
"thiamine pyrophosphate-dependent enzyme", "VOC family protein",
"GntR family transcriptional regulator", "acyl-CoA dehydrogenase family protein",
"flavin reductase family protein", "RidA family protein",
"M24 family metallopeptidase", "LacI family transcriptional regulator",
"NAD(P)-dependent oxidoreductase"), protein_id = c("extdb:LBN7-1.2_001106",
"extdb:LBN7-1.2_001107", "extdb:LBN7-1.2_001108", "extdb:LBN7-1.2_001109",
"extdb:LBN7-1.2_001110", "extdb:LBN7-1.2_001111", "extdb:LBN7-1.2_001112",
"extdb:LBN7-1.2_001113", "extdb:LBN7-1.2_001114", "extdb:LBN7-1.2_001115",
NA, "extdb:LBN7-1.2_001117", "extdb:LBN7-1.2_001118", "extdb:LBN7-1.2_001119",
"extdb:LBN7-1.2_001120", "extdb:LBN7-1.2_001121", "extdb:LBN7-1.2_001122",
"extdb:LBN7-1.2_001123", "extdb:LBN7-1.2_001124", "extdb:LBN7-1.2_001125",
"extdb:LBN7-1.2_001126", "extdb:LBN7-1.2_001127", "extdb:LMX7-1.2_002664",
"extdb:LMX7-1.2_002665", "extdb:LMX7-1.2_002666", "extdb:LMX7-1.2_002667",
"extdb:LMX7-1.2_002668", "extdb:LMX7-1.2_002669", "extdb:LMX7-1.2_002670",
"extdb:LMX7-1.2_002671", "extdb:LMX7-1.2_002672", "extdb:LMX7-1.2_002673",
"extdb:LMX7-1.2_002674", "extdb:LMX7-1.2_002675", "extdb:LMX7-1.2_002676"
), transl_table = c("11", "11", "11", "11", "11", "11", "11",
"11", "11", "11", "11", "11", "11", "11", "11", "11", "11",
"11", "11", "11", "11", "11", "11", "11", "11", "11", "11",
"11", "11", "11", "11", "11", "11", "11", "11"), Ontology_term = c(NA,
NA, NA, NA, NA, NA, NA, NA, "GO:0016624", NA, NA, NA, NA,
NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "GO:0016624",
NA, NA, NA, NA, NA, NA, NA, NA), go_function = c(NA, NA,
NA, NA, NA, NA, NA, NA, "oxidoreductase activity%2C acting on the aldehyde or oxo group of donors%2C disulfide as acceptor|0016624||IEA",
NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
NA, NA, "oxidoreductase activity%2C acting on the aldehyde or oxo group of donors%2C disulfide as acceptor|0016624||IEA",
NA, NA, NA, NA, NA, NA, NA, NA), gene_name = c(NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_), go_process = c(NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_), go_component = c(NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_), Note = c(NA, NA, NA, NA, NA,
NA, NA, NA, NA, NA, "frameshifted", NA, NA, NA, NA, NA, NA,
NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
NA, NA, NA), pseudo = c(NA, NA, NA, NA, NA, NA, NA, NA, NA,
NA, "true", NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA), anticodon = c(NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_), bound_moiety = c(NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_), regulatory_class = c(NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_), gene_synonym = c(NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_), end_range = c(NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, NA_character_), gene_number = c(1106, 1107,
1108, 1109, 1110, 1111, 1112, 1113, 1114, 1115, 1116, 1117,
1118, 1119, 1120, 1121, 1122, 1123, 1124, 1125, 1126, 1127,
2664, 2665, 2666, 2667, 2668, 2669, 2670, 2671, 2672, 2673,
2674, 2675, 2676), width = c(866L, 1076L, 1256L, 389L, 563L,
1202L, 668L, 542L, 2177L, 1310L, 1381L, 623L, 1244L, 1097L,
1511L, 1061L, 962L, 953L, 1382L, 1196L, 455L, 335L, 335L,
1214L, 1382L, 1301L, 2177L, 542L, 668L, 1286L, 563L, 389L,
1256L, 1055L, 866L), length = c(866L, 1076L, 1256L, 389L,
563L, 1202L, 668L, 542L, 2177L, 1310L, 1381L, 623L, 1244L,
1097L, 1511L, 1061L, 962L, 953L, 1382L, 1196L, 455L, 335L,
335L, 1214L, 1382L, 1301L, 2177L, 542L, 668L, 1286L, 563L,
389L, 1256L, 1055L, 866L)), row.names = c(NA, -35L), class = c("tbl_df",
"tbl", "data.frame"))
gff_subs_seqs <- structure(list(seq_id = structure(1:2, .Label = c("LBN7-1_scf1",
"LMX7-1_scf1", "LMX7-1_scf2"), class = "factor"), start = c(0L,
0L), end = c(25141L, 14431L), length = c(25141L, 14431L)), class = "data.frame", row.names = c(NA,
-2L))
gene_links <- structure(list(feat_id = c("LBN7-1.2_001106", "LBN7-1.2_001107",
"LBN7-1.2_001108", "LBN7-1.2_001109", "LBN7-1.2_001109", "LBN7-1.2_001110",
"LBN7-1.2_001111", "LBN7-1.2_001111", "LBN7-1.2_001112", "LBN7-1.2_001113",
"LBN7-1.2_001114", "LBN7-1.2_001115", "LBN7-1.2_001118", "LBN7-1.2_001118",
"LBN7-1.2_001124", "LBN7-1.2_001125", "LBN7-1.2_001125", "LBN7-1.2_001127",
"LBN7-1.2_001127"), feat_id2 = c("LMX7-1.2_002676", "LMX7-1.2_002675",
"LMX7-1.2_002674", "LMX7-1.2_002673", "LMX7-1.2_002664", "LMX7-1.2_002672",
"LMX7-1.2_002671", "LMX7-1.2_002665", "LMX7-1.2_002670", "LMX7-1.2_002669",
"LMX7-1.2_002668", "LMX7-1.2_002667", "LMX7-1.2_002665", "LMX7-1.2_002671",
"LMX7-1.2_002674", "LMX7-1.2_002671", "LMX7-1.2_002665", "LMX7-1.2_002664",
"LMX7-1.2_002673"), pident = c(82.6, 76.6, 97.6, 94.6, 47.8,
95.2, 92, 29.6, 91, 92.8, 96, 87.4, 93.6, 32.9, 52.9, 66, 32.6,
86.5, 48.3), length = c(288L, 351L, 418L, 129L, 115L, 187L, 400L,
402L, 222L, 180L, 725L, 436L, 404L, 395L, 427L, 400L, 390L, 111L,
116L), mismatch = c(50L, 81L, 10L, 7L, 55L, 9L, 32L, 252L, 20L,
13L, 29L, 52L, 26L, 248L, 179L, 134L, 252L, 15L, 55L), gapopen = c(0L,
1L, 0L, 0L, 1L, 0L, 0L, 7L, 0L, 0L, 0L, 1L, 0L, 6L, 2L, 1L, 3L,
0L, 1L), start = c(0L, 871L, 2092L, 3598L, 3598L, 4028L, 4649L,
4649L, 6013L, 6689L, 7387L, 9567L, 13217L, 13217L, 21049L, 22577L,
22577L, 24806L, 24806L), end = c(866L, 1947L, 3348L, 3987L, 3987L,
4591L, 5851L, 5851L, 6681L, 7231L, 9564L, 10877L, 14461L, 14461L,
22431L, 23773L, 23773L, 25141L, 25141L), start2 = c(13565L, 12472L,
11074L, 10422L, 0L, 9819L, 8477L, 758L, 7734L, 7184L, 4852L,
3548L, 758L, 8477L, 11074L, 8477L, 758L, 0L, 10422L), end2 = c(14431L,
13527L, 12330L, 10811L, 335L, 10382L, 9763L, 1972L, 8402L, 7726L,
7029L, 4849L, 1972L, 9763L, 12330L, 9763L, 1972L, 335L, 10811L
), evalue = c(6.7e-126, 6.4e-150, 8e-245, 1.5e-64, 6.9e-22, 2.7e-99,
2.3e-209, 3e-47, 2.1e-111, 3.4e-99, 0, 8.7e-202, 7.2e-222, 2.4e-52,
1.1e-130, 6.8e-153, 1.1e-57, 6.8e-50, 2.4e-23), bitscore = c(444.1,
524.2, 839.7, 239.2, 97.4, 355.1, 721.8, 183.3, 395.6, 354.8,
1402.5, 696.8, 763.5, 200.3, 460.7, 534.3, 218, 190.3, 102.1),
seq_id = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), .Label = c("LBN7-1_scf1",
"LMX7-1_scf1", "LMX7-1_scf2"), class = "factor"), seq_id2 = structure(c(2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L), .Label = c("LBN7-1_scf1", "LMX7-1_scf1", "LMX7-1_scf2"
), class = "factor"), start_feat_id1 = c(0L, 871L, 2092L,
3598L, 3598L, 4028L, 4649L, 4649L, 6013L, 6689L, 7387L, 9567L,
13217L, 13217L, 21049L, 22577L, 22577L, 24806L, 24806L),
end_feat_id1 = c(866L, 1947L, 3348L, 3987L, 3987L, 4591L,
5851L, 5851L, 6681L, 7231L, 9564L, 10877L, 14461L, 14461L,
22431L, 23773L, 23773L, 25141L, 25141L), start_feat_id2 = c(13565L,
12472L, 11074L, 10422L, 0L, 9819L, 8477L, 758L, 7734L, 7184L,
4852L, 3548L, 758L, 8477L, 11074L, 8477L, 758L, 0L, 10422L
), end_feat_id2 = c(14431L, 13527L, 12330L, 10811L, 335L,
10382L, 9763L, 1972L, 8402L, 7726L, 7029L, 4849L, 1972L,
9763L, 12330L, 9763L, 1972L, 335L, 10811L)), row.names = c(NA,
-19L), class = c("tbl_df", "tbl", "data.frame"))
from gggenomes.
Hi Marco,
thanks for giving gggenomes a try and for reporting your issue. You are right, a good documentation on how to generate links from data.frames is missing.
I think the problem here is with the "strandness" of your initial links. You can see it in your first figure with the genomes in opposite directions. The links between genes on different strands should look like "X" not "||".
Blast doesn't encode "strand" explicitly, but by having start > end
for a hit. In your data.frame the start
of the gene on the reverse strand should be greater than the end
. Then those links become "||" after flipping.
# change "strand" of gene links by switching start and end
gene_links2 <- gene_links %>% rename(start2=end2, end2=start2)
# get "crossed" links for genes pairs on different strands
p2 <- p %>% add_links(gene_links2) + geom_link()
p2
# get proper parallel links after flipping
p2 %>% flip(2)
Hope that helps! Also, if you want to share more about your initial workflow to figure out why this happened and how to avoid it, let me know.
from gggenomes.
Hi Thomas
Thanks for you prompt reply. Yes, that solved the problem. I have no idea what caused this. In fact, when scaling up to include more samples, it worked just fine. However, I was able to change the direction of a few genomes (and change the start2 end2) which worked as you showed above.
from gggenomes.
Related Issues (20)
- Draw links as single lines? HOT 4
- Overlapping text lables HOT 2
- Error in `geom_link()`: HOT 7
- geom_feat size and position not responding HOT 3
- geom_link new error HOT 2
- Strand error when call gggenome()
- Submission for JOSS?
- Errror while installing HOT 1
- ggplot2 error using example data HOT 6
- Installation error HOT 3
- fill and fontface otions for geom_gene_label HOT 4
- Move deps from Depends to Imports? HOT 1
- Adding UTRs in the plot HOT 3
- Genes do not start and end at the expected positions HOT 2
- Setting coordinates to visualise part of the genome HOT 1
- shitf() "unused argument" HOT 2
- geom_gene() doesn't work HOT 5
- Errors when running read_feats command HOT 3
- Change space between seqs within the same bin HOT 5
- Changing gene colours HOT 2
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from gggenomes.