README.md

In JakeConway/ClinPlots: ClinPlots

ClinPlots

An R package to create clinico-genomic charts

There is a need to rapidly and effectively summarize multivariate risk information for patients and physicians. Many visualizations that accomplish this task are exhibited in the paper Clinical assessment incorporating a personal genome, which provides the motivation for developing this package. Two examples of these figures can be seen below, whose reproduction will become automated through this package.

Install the package using:

devtools::github_install("JakeConway/ClinPlots")

A sample script to generate both plots, using the data above:

require(ggplot2)
require(scales)
require(gridExtra)
require(grid)
library(ClinPlots)

cr_df <- read.csv(system.file("extdata", "clinical_risk.txt", package = "ClinPlots"), sep='\t')
disorderCohortRiskPlot(cr_df)

MI_df <- read.csv(system.file("extdata", "MI_genomic_risk.txt", package = "ClinPlots"), sep='\t')
genomicRiskSummaryPlot(MI_df, "pt_probability") #running genomicRiskSummaryPlot(MI_df, 7) will produce same result

JakeConway/ClinPlots documentation built on May 7, 2019, 10:19 a.m.