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plot.sccomp_tbl.Rd
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plot.sccomp_tbl.Rd
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% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/methods.R
\name{plot.sccomp_tbl}
\alias{plot.sccomp_tbl}
\title{plot}
\usage{
\method{plot}{sccomp_tbl}(
x,
significance_threshold = 0.05,
test_composition_above_logit_fold_change = attr(.data,
"test_composition_above_logit_fold_change"),
...
)
}
\arguments{
\item{x}{A tibble including a cell_group name column | sample name column | read counts column | factor columns | Pvalue column | a significance column}
\item{significance_threshold}{Numeric value specifying the significance threshold for highlighting differences. Default is 0.025.}
\item{test_composition_above_logit_fold_change}{A positive integer. It is the effect threshold used for the hypothesis test. A value of 0.2 correspond to a change in cell proportion of 10\% for a cell type with baseline proportion of 50\%. That is, a cell type goes from 45\% to 50\%. When the baseline proportion is closer to 0 or 1 this effect thrshold has consistent value in the logit uncontrained scale.}
\item{...}{For internal use}
}
\value{
A \code{ggplot}
}
\description{
This function plots a summary of the results of the model.
}
\examples{
message("Use the following example after having installed install.packages(\"cmdstanr\", repos = c(\"https://stan-dev.r-universe.dev/\", getOption(\"repos\")))")
\donttest{
if (instantiate::stan_cmdstan_exists()) {
data("counts_obj")
estimate = sccomp_estimate(
counts_obj,
~ type, ~1, sample, cell_group, count,
cores = 1
)
# estimate |> plot()
}
}
}