plotPrevalenceOverTime: Plot daily prevalence of a lineage by location

In outbreak-info/R-outbreak-info: outbreak.info R Client

Plot daily prevalence of a lineage by location

Description

Plots the daily prevalence of a PANGO lineage by location

Usage

plotPrevalenceOverTime(
  df,
  colorVar = "lineage",
  title = "Prevalence over time",
  labelDictionary = NULL
)

Arguments

df	result of the call to getPrevalence
colorVar	variable to used to color the line traces. 'lineage' by default
title	(optional) Title to add to the plot
labelDictionary	(optional) a named list of values to replace in the plot legend.

Value

ggplot2 object

Examples

p1_brazil <- getPrevalence(pangolin_lineage = "P.1", location = "Brazil")
plotPrevalenceOverTime(p1_brazil)

us <- getPrevalence(pangolin_lineage = c("B.1.1.7", "B.1.427 OR B.1.429", "B.1.617.2"), location = "United States")
plotPrevalenceOverTime(us, labelDictionary = c("B.1.427 OR B.1.429" = "Epsilon"))

# Overlay locations
b117_india = getPrevalence(pangolin_lineage = "B.1.1.7", location = "India")
b117_us = getPrevalence(pangolin_lineage = "B.1.1.7", location = "United States")
b117_uk = getPrevalence(pangolin_lineage = "B.1.1.7", location = "United Kingdom")
b117 = dplyr::bind_rows(b117_uk, b117_india, b117_us)
plotPrevalenceOverTime(b117, colorVar = "location", title="B.1.1.7 prevalence over time")

outbreak-info/R-outbreak-info documentation built on March 2, 2023, 9:58 a.m.