plotKdModel: plotKdModel

In ETHZ-INS/scanMiR: scanMiR

plotKdModel

Description

Plots the summary of an affinity model.

Usage

plotKdModel(mod, what = c("both", "seeds", "logo"), n = 10)

Arguments

mod	A 'KdModel'
what	Either 'seeds', 'logo', or 'both' (default).
n	The number of top 7-mers to plot (when ‘what=’seeds'')

Details

‘what=’seeds'' plots the -$log(K_d)$ 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, oriented in the direction of the target mRNA). 'what="both"' plots both. Note that if the package 'ggseqlogo' is installed, this will be used instead to plot the logo, resulting in more detailed plot annotation.

Value

If 'what="logo"', returns nothing and plots a position weight matrix. Otherwise returns a ggplot.

Examples

data(SampleKdModel)
plotKdModel(SampleKdModel, what="seeds")

ETHZ-INS/scanMiR documentation built on April 16, 2024, noon