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plots: Add rankings plot

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This commit is contained in:
Elias Projahn 2021-12-02 15:28:03 +01:00
parent 2c15ba55c1
commit f997b5fdd7
4 changed files with 100 additions and 7 deletions
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23
man/plot_rankings.Rd Normal file
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@ -0,0 +1,23 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/plots.R
\name{plot_rankings}
\alias{plot_rankings}
\title{Plot a side-by-side comparison of multiple rankings.}
\usage{
plot_rankings(rankings, gene_sets)
}
\arguments{
\item{rankings}{A named list of rankings to display. The names will be shown
as labels in the plot.}
\item{gene_sets}{A named list of vectors of gene IDs to highlight. The names
will be used to distinguish the sets and in the legend.}
}
\description{
Each ranking's scores will be shown as a vertical violin plot without any
additional markings. The gene sets will be shown as markers on top of the
density visualization.
}
\details{
This function requires the package \code{plotly}.
}

10
man/preset.Rd
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@ -5,7 +5,7 @@
\title{Create a new preset.}
\usage{
preset(
methods = c("clusteriness", "correlation", "neural", "proximity"),
methods = c("clusteriness", "correlation", "neural", "adjacency", "proximity"),
species_ids = NULL,
gene_ids = NULL,
reference_gene_ids = NULL,
@ -40,14 +40,10 @@ Available methods are:
\itemize{
\item \code{clusteriness} How much the gene distances to the nearest telomere
cluster across species.
\item \code{clusteriness_positions} The same as \code{clusteriness} but using absolute
gene positions instead of distances.
\item \code{correlation} The mean correlation of gene distances to the nearest
telomere across species.
\item \code{correlation_positions} Correlation using position data.
\item \code{neural} Assessment by neural network trained using distances.
\item \code{neural_positions} Assessment by neural network trained using absolute
position data.
\item \code{neural} Assessment by neural network trained on the reference genes.
\item \code{adjacency} Proximity to reference genes.
\item \code{proximity} Mean proximity to telomeres.
}