Man pages for thackl/gggenomes
A Grammar of Graphics for Comparative Genomics

add_tracksAdd different types of tracks
anchorThe virtual x-start of the full length seq in the plot
as_featsCompute a layout for feat data
as_linksCompute a layout for link data
as_seqsCompute a layout for sequence data
as_subfeatsCompute a layout for subfeat data
as_sublinksCompute a layout for links linking feats
as_tracksConvert a list of tibbles into tracks with magic
commaCollapse a string with commas
def_formatsDefined file formats and extensions
def_namesDefault column names and types for defined formats
dim.gggenomes_layout'ggplot2::facet_null' checks data with 'empty(df)' using...
emale_avaAll-versus-all whole genome alignments of 6 EMALE genomes
emale_cogsClusters of orthologs of 6 EMALE proteomes
emale_gcRelative GC-content along 6 EMALE genomes
emale_genesGene annotations if 6 EMALE genomes (endogenous virophages)
emale_ngarosIntegrated Ngaro retrotransposons of 6 EMALE genomes
emale_prot_avaAll-versus-all alignments 6 EMALE proteomes
emale_prot_uniref50Alignments of 6 EMALE proteomes against Uniref50
emale_seqsSequence index of 6 EMALE genomes (endogenous virophages)
emale_tirsTerminal inverted repeats of 6 EMALE genomes
exGet path to gggenomes example files
file_labelAdd a unique name to files
flipFlip bins and sequences
focusShow features and regions of interest
geom_bin_labelDraw bin labels
geom_featDraw feats
geom_feat_textAdd text to genes, features, etc.
geom_geneDraw gene models
geom_gene_labeldraw feat labels
geom_linkDraw links
geom_link_labeldraw link labels
geom_seqdraw seqs
geom_seq_labeldraw feat labels
geom_wiggleDraw wiggle ribbons or lines
get_seqsGet/set the seqs track
gggenomesPlot genomes, features and synteny maps
ggplot.gggenomes_layoutggplot.default tries to 'fortify(data)' and we don't want...
has_varsCheck if variables exist in object
in_rangeDo numeric values fall into specified ranges?
introduceIntroduce non-existing columns
layoutRe-layout a genome layout
layout_featsLayout feats
layout_genomesLayout genomes
layout_linksLayout tbl_link
layout_seqsLayout sequences
match_argmatch.arg defaulting to all choices
pickPick bins and seqs by name or position
position_strandStack features
pull_trackUse tracks inside and outside geom_* calls
read_alitvRead AliTV .json file
read_bedRead a BED file
read_blastRead BLAST tab-separated output
read_contextRead files in different contexts
read_gbkRead genbank files
read_gff3Read features from GFF3 (and with some limitations GFF2/GTF)...
read_pafRead a .paf file (minimap/minimap2).
read_seq_lenRead sequence index
read_tracksRead files in various standard formats (FASTA, GFF3, GBK,...
reexportsObjects exported from other packages
require_varsRequire variables in an object
scale_x_bpX-scale for genomic data
shiftShift bins left/right
swap_ifSwap values of two columns based on a condition
swap_querySwap query and subject in blast-like feature tables
theme_gggenomes_cleangggenomes default theme
track_idsNamed vector of track ids and types
track_infoBasic info on tracks in a gggenomes object
track_nrowsNumber of rows of all tracks tables
track_typeTrack type by track id
track_typesAll types of all tracks
vars_trackTidyselect track variables
vars_track_errorError messages for vars_track
widthThe width of a range
write_gff3Write a gff3 file from a tidy table
xProject feat coordinates into layout space
thackl/gggenomes documentation built on Nov. 8, 2021, 8:50 a.m.