Merge pull request #6 from thackl/develop

Develop

.gitignore

@@ -2,4 +2,9 @@
 .Rhistory
 .RData
 docs/
-org/
+org/
+R-deprecated/
+data-raw/
+exec/
+tests/
+vignettes-manual-export/

DESCRIPTION

@@ -15,7 +15,8 @@ URL: https://github.com/thackl/gggenomes
 BugReports: https://github.com/thackl/gggenomes/issues
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.1.0
+RoxygenNote: 7.1.1
+Roxygen: list(markdown = TRUE)
 Remotes: github::thackl/thacklr, bioc::release/rtracklayer
 Depends:
     R (>= 3.4.2),
@@ -25,6 +26,7 @@ Depends:
     purrr,
     readr,
     stringr,
+    tidyr,
     thacklr,
     tibble,
     jsonlite

NAMESPACE

@@ -1,28 +1,26 @@
 # Generated by roxygen2: do not edit by hand
 
-S3method("seqs<-",gggenomes)
-S3method("seqs<-",gggenomes_layout)
 S3method(activate,tbl_genome_layout)
 S3method(add_clusters,gggenomes)
 S3method(add_clusters,gggenomes_layout)
-S3method(add_features,gggenomes)
-S3method(add_features,gggenomes_layout)
+S3method(add_feats,gggenomes)
+S3method(add_feats,gggenomes_layout)
 S3method(add_links,gggenomes)
 S3method(add_links,gggenomes_layout)
 S3method(add_seqs,gggenomes)
 S3method(add_seqs,gggenomes_layout)
-S3method(add_subfeatures,gggenomes)
-S3method(add_subfeatures,gggenomes_layout)
+S3method(add_subfeats,gggenomes)
+S3method(add_subfeats,gggenomes_layout)
 S3method(add_sublinks,gggenomes)
 S3method(add_sublinks,gggenomes_layout)
-S3method(as_features,default)
-S3method(as_features,tbl_df)
+S3method(as_feats,default)
+S3method(as_feats,tbl_df)
 S3method(as_links,default)
 S3method(as_links,tbl_df)
 S3method(as_seqs,default)
 S3method(as_seqs,tbl_df)
-S3method(as_subfeatures,default)
-S3method(as_subfeatures,tbl_df)
+S3method(as_subfeats,default)
+S3method(as_subfeats,tbl_df)
 S3method(as_sublinks,default)
 S3method(as_sublinks,tbl_df)
 S3method(as_tibble,GRanges)
@@ -35,25 +33,33 @@ S3method(flip,gggenomes)
 S3method(flip,gggenomes_layout)
 S3method(flip_nicely,gggenomes)
 S3method(flip_nicely,gggenomes_layout)
-S3method(flip_seq,gggenomes)
-S3method(flip_seq,gggenomes_layout)
+S3method(flip_seqs,gggenomes)
+S3method(flip_seqs,gggenomes_layout)
 S3method(flip_strand,character)
 S3method(flip_strand,logical)
 S3method(flip_strand,numeric)
+S3method(get_seqs,gggenomes)
+S3method(get_seqs,gggenomes_layout)
+
 S3method(ggplot,gggenomes_layout)
 S3method(layout,gggenomes)
 S3method(layout,gggenomes_layout)
-S3method(makeContent,cdsarrowtree)
-S3method(pull_features,gggenomes)
-S3method(pull_features,gggenomes_layout)
+S3method(makeContent,genetree)
+S3method(print,gggenomes_layout)
+S3method(pull_bins,gggenomes)
+S3method(pull_bins,gggenomes_layout)
+S3method(pull_feats,gggenomes)
+S3method(pull_feats,gggenomes_layout)
+S3method(pull_genes,gggenomes)
+S3method(pull_genes,gggenomes_layout)
 S3method(pull_links,gggenomes)
 S3method(pull_links,gggenomes_layout)
 S3method(pull_seqs,gggenomes)
 S3method(pull_seqs,gggenomes_layout)
 S3method(pull_track,gggenomes)
 S3method(pull_track,gggenomes_layout)
-S3method(seqs,gggenomes)
-S3method(seqs,gggenomes_layout)
+S3method(set_seqs,gggenomes)
+S3method(set_seqs,gggenomes_layout)
 S3method(strand_chr,character)
 S3method(strand_chr,factor)
 S3method(strand_chr,logical)
@@ -67,84 +73,115 @@ S3method(strand_lgl,logical)
 S3method(strand_lgl,numeric)
 S3method(track_ids,gggenomes)
 S3method(track_ids,gggenomes_layout)
+S3method(track_info,gggenomes)
+S3method(track_info,gggenomes_layout)
 export("%<>%")
 export("%>%")
-export("seqs<-")
+export(GeomFeatText)
 export(PositionPile)
 export(PositionSixframe)
 export(PositionStrand)
 export(PositionStrandpile)
 export(activate)
 export(active)
 export(add_clusters)
-export(add_features)
+export(add_feats)
 export(add_links)
 export(add_seqs)
-export(add_subfeatures)
+export(add_subfeats)
 export(add_sublinks)
-export(as_features)
+export(as_feats)
 export(as_links)
 export(as_seqs)
-export(as_subfeatures)
+export(as_subfeats)
 export(as_sublinks)
+export(bins)
 export(check_strand)
 export(combine_strands)
-export(drop_feature_layout)
+export(def_names)
+export(def_types)
+export(drop_feat_layout)
 export(drop_layout)
 export(drop_link_layout)
 export(drop_seq_layout)
-export(example_files)
-export(example_sets)
+export(ex)
+export(feats)
+export(feats0)
+export(file_formats)
 export(flip)
 export(flip_nicely)
-export(flip_seq)
+export(flip_seqs)
 export(flip_strand)
 export(focus)
+export(genes)
 export(geom_bin_label)
-export(geom_feature)
-export(geom_feature_label)
+export(geom_feat)
+export(geom_feat_label)
+export(geom_feat_note)
+export(geom_feat_tag)
+export(geom_feat_text)
 export(geom_gene)
+export(geom_gene_fast)
 export(geom_gene_label)
+export(geom_gene_note)
+export(geom_gene_tag)
+export(geom_gene_text)
 export(geom_link)
 export(geom_link_label)
 export(geom_seq)
 export(geom_seq_label)
+export(get_seqs)
 export(gggenomes)
 export(has_vars)
 export(if_reverse)
+export(in_range)
+export(introduce)
 export(is_reverse)
 export(layout)
 export(layout_genomes)
 export(layout_seqs)
+export(links)
 export(pick)
 export(pick_at)
 export(pick_bins)
+export(pick_by_tree)
 export(position_pile)
 export(position_sixframe)
 export(position_strand)
 export(position_strandpile)
-export(pull_features)
+export(pull_bins)
+export(pull_feats)
+export(pull_genes)
 export(pull_links)
 export(pull_seqs)
 export(pull_track)
+export(read_bed)
+export(read_fai)
+export(read_feats)
+export(read_gbk)
+export(read_gff3)
+export(read_links)
 export(read_alitv)
-export(read_gffs)
-export(read_gffs_as_contigs)
 export(read_paf)
+export(read_seq_len)
+export(read_seqs)
+export(read_subfeats)
+export(read_sublinks)
 export(require_vars)
+export(scale_x_continuous)
 export(seqs)
+export(set_seqs)
 export(shift)
 export(strand_chr)
 export(strand_int)
 export(strand_lgl)
+export(swap_query)
 export(theme_gggenomes_clean)
 export(track)
 export(track_ids)
-export(use_bins)
-export(use_features)
-export(use_genes)
-export(use_links)
-export(use_seqs)
+export(track_info)
+export(unnest_exons)
+export(write_gff3)
 import(ggplot2)
 import(grid)
 import(rlang)
@@ -160,4 +197,4 @@ importFrom(rlang,quo_text)
 importFrom(thacklr,read_paf)
 importFrom(tibble,as_tibble)
 importFrom(tidyr,unnest)
-importFrom(tidyr,unnest_wider)
+importFrom(tidyr,unnest_wider)