gglogo: Geom for Logo Sequence Plots

Visualize sequences in (modified) logo plots. The design choices used by these logo plots allow sequencing data to be more easily analyzed. Because it is integrated into the 'ggplot2' geom framework, these logo plots support native features such as faceting.

Author
Heike Hofmann [aut], Eric Hare [aut, cre], GGobi Foundation [aut]
Date of publication
2016-06-29 02:44:46
Maintainer
Eric Hare <erichare@iastate.edu>
License
GPL-3
Version
0.1.2
URLs

View on CRAN

Man pages

aacids
properties of amino acids
alphabet
alphabet polygon data
calcInformation
Compute shannon information based on position and treatment
createPolygons
Create a data set of polygons for a set of letters from a...
determineOrder
Determine order in which to pass through a set of points
fortify
Convert image matrix to a data frame
geom_logo
Sequence logo plots.
getOutline
Determine boundary between foreground and background in an...
ggfortify
Convert sequence data to a format suitable for logo plots
identifyParts
Identify different parts of a polygon
letterObject
Convert a text element into an R object
letterToPolygon
Convert an image file to a polygon
logo
Logo plot
mainPlusIslands
Set the orientation of a polygon
point_line_dist
Distance between point and line
position_logo
Logo positioning for overlapping objects on top of one...
sequences
peptide sequence data
simplifyPolygon
Douglas-Peucker algorithm adjusted fo polyons
simplify_rec
Douglas Pecker algorithm for line thinning
splitSequence
Reshape data set according to elements in sequences
stat_logo
Calculation of all pieces necessary to plot a logo sequence...

Files in this package

gglogo
gglogo/inst
gglogo/inst/cluster.r
gglogo/inst/visual_test
gglogo/inst/visual_test/vtest
gglogo/inst/visual_test/vtest/images
gglogo/inst/visual_test/vtest/images/d93cc0a152e33496651c840f13bbcd8e
gglogo/inst/visual_test/vtest/images/97a8db6e1b341d10f3619e012110beb0
gglogo/inst/visual_test/vtest/images/e8ee76302992cdf08c555066fc33472c
gglogo/inst/visual_test/vtest/images/6d176252c1f71753984e9b31bb16375a
gglogo/inst/visual_test/vtest/resultsets.csv
gglogo/inst/visual_test/vtest/commits.csv
gglogo/inst/visual_test/logos.R
gglogo/NAMESPACE
gglogo/data
gglogo/data/aacids.RData
gglogo/data/aacids.rda
gglogo/data/alphabet.rda
gglogo/data/sequences.rda
gglogo/R
gglogo/R/text.r
gglogo/R/alphabet.r
gglogo/R/thin.r
gglogo/R/logos.r
gglogo/R/data.r
gglogo/R/position.r
gglogo/MD5
gglogo/DESCRIPTION
gglogo/man
gglogo/man/fortify.Rd
gglogo/man/position_logo.Rd
gglogo/man/letterToPolygon.Rd
gglogo/man/mainPlusIslands.Rd
gglogo/man/logo.Rd
gglogo/man/splitSequence.Rd
gglogo/man/createPolygons.Rd
gglogo/man/stat_logo.Rd
gglogo/man/simplify_rec.Rd
gglogo/man/sequences.Rd
gglogo/man/aacids.Rd
gglogo/man/simplifyPolygon.Rd
gglogo/man/ggfortify.Rd
gglogo/man/point_line_dist.Rd
gglogo/man/letterObject.Rd
gglogo/man/determineOrder.Rd
gglogo/man/alphabet.Rd
gglogo/man/identifyParts.Rd
gglogo/man/calcInformation.Rd
gglogo/man/getOutline.Rd
gglogo/man/geom_logo.Rd