as_links: Compute a layout for link data
In thackl/gggenomes: A Grammar of Graphics for Comparative Genomics
as_links R Documentation
Compute a layout for link data
Description
Read link data of pairwise sequence or feat comparisons, such as
similarity searches into a tidy dataframe and augment it with layout
information based on a sequence layout.
Usage
as_links(x, seqs, ..., everything = TRUE)
Arguments
x
link data convertible to a link layout
seqs
the sequence layout the feat map onto.
...
passed on to layout_seqs()
everything
set to FALSE to drop optional columns
Details
Obligatory columns are seq_id and seq_id2. Also recognized are
start, end,start2,end2,strand, bin_idandbin_id2.
During layouting, seq_id,start,end will be projected to x,xend,y, while
seq_id2,start2,end2 will be projected to xmin,xmax,yend. gggenomes uses these
maybe a bit odd names for the variables here, is so that they play nice with
ggplots native transformation functions for position aesthetics. Those only
work well with a specific set of predefined var names, which include those
used above.
thackl/gggenomes documentation built on March 10, 2024, 7:26 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
| as_links | R Documentation |
Compute a layout for link data
Description
Read link data of pairwise sequence or feat comparisons, such as similarity searches into a tidy dataframe and augment it with layout information based on a sequence layout.
Usage
as_links(x, seqs, ..., everything = TRUE)
Arguments
x |
link data convertible to a link layout |
seqs |
the sequence layout the feat map onto. |
... |
passed on to |
everything |
set to FALSE to drop optional columns |
Details
Obligatory columns are seq_id and seq_id2. Also recognized are
start, end,start2,end2,strand, bin_idandbin_id2.
During layouting, seq_id,start,end will be projected to x,xend,y, while seq_id2,start2,end2 will be projected to xmin,xmax,yend. gggenomes uses these maybe a bit odd names for the variables here, is so that they play nice with ggplots native transformation functions for position aesthetics. Those only work well with a specific set of predefined var names, which include those used above.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.