Package: ggseqlogo 0.1

Omar Wagih

ggseqlogo: A 'ggplot2' Extension for Drawing Publication-Ready Sequence Logos

The extensive range of functions provided by this package makes it possible to draw highly versatile sequence logos. Features include, but not limited to, modifying colour schemes and fonts used to draw the logo, generating multiple logo plots, and aiding the visualisation with annotations. Sequence logos can easily be combined with other plots 'ggplot2' plots.

Authors:Omar Wagih

ggseqlogo_0.1.tar.gz
ggseqlogo_0.1.zip(r-4.5)ggseqlogo_0.1.zip(r-4.4)ggseqlogo_0.1.zip(r-4.3)
ggseqlogo_0.1.tgz(r-4.4-any)ggseqlogo_0.1.tgz(r-4.3-any)
ggseqlogo_0.1.tar.gz(r-4.5-noble)ggseqlogo_0.1.tar.gz(r-4.4-noble)
ggseqlogo_0.1.tgz(r-4.4-emscripten)ggseqlogo_0.1.tgz(r-4.3-emscripten)
ggseqlogo.pdf |ggseqlogo.html✨
ggseqlogo/json (API)

# Install 'ggseqlogo' in R:

install.packages('ggseqlogo', repos = c('https://blaserlab.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/omarwagih/ggseqlogo/issues

Datasets:

pfms_dna - List of position frequency matrices for transcription factors
seqs_aa - List of aligned kinase-substrate binding sequences
seqs_dna - List of aligned transcription factor binding sequences

On CRAN:

11.64 score 207 stars 10 packages 732 scripts 3.2k downloads 49 mentions 6 exports 28 dependencies

Last updated 1 months agofrom:9c26c0b205. Checks:OK: 5 NOTE: 2. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Nov 12 2024
R-4.5-win	NOTE	Nov 12 2024
R-4.5-linux	NOTE	Nov 12 2024
R-4.4-win	OK	Nov 12 2024
R-4.4-mac	OK	Nov 12 2024
R-4.3-win	OK	Nov 12 2024
R-4.3-mac	OK	Nov 12 2024

Exports:geom_logo ggseqlogo list_col_schemes list_fonts make_col_scheme theme_logo

Dependencies:cli colorspace fansi farver ggplot2 glue gtable isoband labeling lattice lifecycle magrittr MASS Matrix mgcv munsell nlme pillar pkgconfig R6 RColorBrewer rlang scales tibble utf8 vctrs viridisLite withr

ggseqlogo introduction

Omar Wagih

Rendered fromggseqlogo_introduction.Rmdusingknitr::rmarkdownon Nov 12 2024.

Last update: 2023-11-26
Started: 2017-06-13

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Plots sequence logo as a layer on ggplot	geom_logo
Quick sequence logo plot	ggseqlogo
List color schemes available in ggseqlogo	list_col_schemes
List fonts available in ggseqlogo	list_fonts
Create new sequence logo color scheme	make_col_scheme
List of position frequency matrices for transcription factors	pfms_dna
List of aligned kinase-substrate binding sequences	seqs_aa
List of aligned transcription factor binding sequences	seqs_dna
ggseqlogo custom theme	theme_logo