DepLogo v1.0

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Dependency Logo

Plots dependency logos from a set of input sequences.

Functions in DepLogo

Name Description
logo Sequence logo
plotBlocks Plots blocks of data
getDeps Compute dependencies between positions
plotDepmatrix Plot a matrix representation of dependency values.
plotDeplogo Plot a dependency logo
plotDeparcs Plot a graph representation of dependency values.
filterColumns Filter data columns by some filter function
filter.by.gaps Filter columns (sequence positions) by gaps
replaceColors Replace colors in DLData object
alphabet.protein.gap Amino acid alphabet with gaps
filter.by.conservation Filter columns (sequence positions) by conservation
revcom Reverse complement
subBoxes Plot weights as boxplots
filter.by.dependencies Filter columns (sequence positions) by dependency
subLines Plot weights as lines
partition Parition data by most inter-dependent positions
getPWM Position weight matrix from DLData object
suggestColors Suggest colors for symbols
summary.DLData Summarizing DLData objects
colorchart Plot a colorchart representation of a set of sequences.
alphabet.rna RNA alphabet
alphabet.protein Amino acid alphabet
alphabet.dna.gap DNA alphabet with gaps
alphabet.dna DNA alphabet
alphabet.rna.gap RNA alphabet with gaps
Alphabet built alphabet
deprects Rectangles of averaged colors
DLData Create DLData object
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Vignettes of DepLogo

Name
DepLogo.Rmd
annotated_deplogo.png
references.bib
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Details

Type Package
License GPL-3
NeedsCompilation no
RoxygenNote 6.0.1
VignetteBuilder knitr
Packaged 2019-03-13 13:30:19 UTC; dev
Repository CRAN
Date/Publication 2019-03-13 16:23:27 UTC

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