plotKdModel {scanMiR} | R Documentation |
Plots the summary of an affinity model.
plotKdModel(mod, what = c("both", "seeds", "logo"), n = 10)
mod |
A 'KdModel' |
what |
Either 'seeds', 'logo', or 'both' (default). 'logo' and 'both |
n |
The number of top 7-mers to plot (when ‘what=’seeds'') |
‘what=’seeds'' plots the -log(Kd) values of the top 'n' 7-mers (including both canonical and non-canonical sites), with or without the final "A" vis-a-vis the first miRNA nucleotide. ‘what=’logo'' plots a 'seqLogo' (requires the [seqLogo](https://bioconductor.org/packages/release/bioc/html/seqLogo.html) package) showing the nucleotide-wise information content and preferences for all 12-mers (centered around the seed). 'what="both"' plots both.
If 'what="logo"', returns nothing a plots a position weight matrix. Otherwise returns a ggplot.
data(SampleKdModel) plotKdModel(SampleKdModel, what="seeds")