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A ggplot2-based R package for visualizing longitudinal patient data and integrated clinical events in a user-friendly and customizable manner.

License: Other

R 100.00%

gglongi's Introduction

gglongi

This package allows you to build longitudinal plots. It was born out of the need to visualize genomic data over time and overlay clinical events such as treatment, scan dates, date of progression and date of death; however, as long as your data has a time component and some continuous value, you can use gglongi in your analysis workflow.

Installation

You can install the development version of gglongi from GitHub with:

# install.packages("devtools")
devtools::install_github("juditkisistok/gglongi")

Example

This is a basic example which shows you how to create a longitudinal plot:

library(gglongi)
data("mafs")
data("treatment")
data("scans")
data("clinical_events")

## basic example code
## colored rectangles represent the type and duration of treatment
## dotted, red and black lines correspond to scan, progression and death dates, respectively

gglongi(mafs, x_val = "time_from_baseline", y_val = "MAF", col_val = "Gene", 
        col_legend = TRUE, mean_line = TRUE, x_title = "Days from baseline sample", 
        y_title = "Mutant allele frequency", treatments = treatment, scans = scans, 
        events = clinical_events, treatment_start = "start_from_baseline", 
        treatment_end = "stop_from_baseline", treatment_drug = "Treatment_drug", 
        scan_date = "Days_from_baseline", event_date = "Days_from_baseline")