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

activateactivate
add_clustersAdd gene clusters
add_featuresAdd features
add_linksAdd links
add_subfeaturesAdd subfeatures
add_sublinksAdd sublinks
anchorThe virtual x-start of the full length seq in the plot
as_featuresCompute a layout for feature data
as_linksCompute a layout for link data
as_seqsCompute a layout for sequence data
as_subfeaturesCompute a layout for subfeature data
as_sublinksCompute a layout for links linking features
dim.gggenomes_layout'ggplot2::facet_null' checks data with 'empty(df)' using...
example_fileslist files from example data sets
example_setsExample data sets
flipFlip bins and sequences
focusFocus on features and regions of interest
geom_bin_labelDraw bin labels
geom_featuredraw features
geom_geneDraw genes
geom_gene_labeldraw feature labels
geom_linkDraw links
geom_link_labeldraw link labels
geom_seqdraw seqs
geom_seq_labeldraw feature labels
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?
layoutRe-layout a genome layout
layout_featuresLayout features
layout_linksLayout tbl_link
pickPick seqs and bins by name or position
position_strandStack features
pull_seqsPull out a specific track, possibly filtered
read_alitvRead AliTV .json file
read_gffsRead .gff files
read_gffs_as_contigsRead genome_ids, contig_ids and contig lengths from .gff...
read_pafread a .paf file (minimap/minimap2). Only the first 12...
reexportsObjects exported from other packages
require_varsRequire variables in an object
seqsGet/set the seqs track
shiftShift bins left/right
swap_ifSwap values of two columns based on a condition
theme_gggenomes_cleangggenomes default theme
use_seqsUse a specific track table inside a 'geom_*' call.
widthThe width of a range
xProject feature coordinates into layout space
thackl/gggenomes documentation built on July 14, 2020, 4 p.m.