Package index • genoPlotR

All functions

annotation() as.annotation() is.annotation(): annotation class and methods

artemisColors(): Artemis Colors

auto_annotate(): Auto-annotate dna_segs

barto: Comparison of 4 Bartonella genomes

best_hit(): Filter a comparison to include only the best hits for each query

bidirectional_best_hit(): Filter a comparison to include only bidirectional best hits

chrY_subseg: Comparisons of subsegments of the Y chromosome in human and chimp

comparison() as.comparison() is.comparison(): comparison class and methods

comparisons_from_dna_segs(): Create comparisons between DNA segments

dna_seg() as.dna_seg() is.dna_seg(): dna_seg class and methods

dna_seg_to_fasta(): Convert dna_seg objects to FASTA files

edit_dna_segs(): Edit dna_seg features

genbank_to_fasta(): Convert GenBank files to FASTA files

gene_types(): Lists gene_types for dna_seg objects

gradient_color_scheme() apply_color_scheme(): Generate a gradient color scheme

human_nt(): Human-readable nucleotide scale

make_unique_ids(): Make unique IDs for dna_segs

mauve_bbone: Mauve backbone of 4 Bartonella genomes

max_by_group(): Filter dna_seg features by looking at a maximum within groups

middle(): Find the middle point of dna_seg features

permute_dna_segs(): Reorder dna_segs or labels to match a tree

plot_gene_map(): Plot gene and genome maps

print_comparison(): Print out a comparison

range(<annotation>) range(<comparison>) range(<dna_seg>): Range calculation

read_comparison_from_file() read_comparison_from_files() read_comparison_from_blast() read_comparison_from_tab(): Creating comparisons between genomic sequences from files

read_dna_seg_from_file() read_dna_seg_from_files() read_dna_seg_from_embl() read_dna_seg_from_genbank() read_dna_seg_from_fasta() read_dna_seg_from_ptt() read_dna_seg_from_tab(): Creating dna_segs from files

read_mauve_backbone(): Read mauve backbone files to create dna_segs and comparisons

read_offsets(): Parse dna_seg offset values for plotting

read_offsets_file(): Parse dna_seg offset values for plotting from a file

read_orthogroup_from_file() read_orthogroup_from_orthomcl() read_orthogroup_from_orthofinder() read_orthogroup_from_mmseqs2() read_orthogroup_from_diamond(): Create comparisons between dna_segs by reading in a file of groupings

read_xlims(): Parse xlims, a set of dna_seg positions for plotting

read_xlims_file(): Parse xlims from a file, a set of dna_seg positions for plotting

reverse(): Reverse objects

run_blast() run_diamond(): Perform sequence alignments using DIAMOND or BLAST

seg_plot() as.seg_plot() is.seg_plot(): seg_plot class and methods

sequential_color_scheme(): Apply a sequential color scheme to dna_segs and comparisons

sequential_updates(): Update dna_segs and comparisons sequentially in plotting order

three_genes: Three genes data set

trim(): Trimming data frames using a numeric interval

trim_tree(): Trim a tree to remove unused sequences

uniform_color_scheme(): Apply a uniform color scheme to dna_segs and comparisons

update_comparisons(): Update comparisons using dna_segs

update_dna_segs(): Update dna_segs using comparisons