Nothing
## ----setup, include=FALSE-----------------------------------------------------
knitr::opts_chunk$set(echo = TRUE)
## ---- warning=FALSE, message=FALSE--------------------------------------------
library(pagoo) # Load package
toy_rds <- system.file('extdata', 'campylobacter.RDS', package = 'pagoo')
p <- load_pangenomeRDS(toy_rds)
## -----------------------------------------------------------------------------
p$dist()
## ---- eval=FALSE--------------------------------------------------------------
# p$dist(method = "jaccard", binary = TRUE)
## -----------------------------------------------------------------------------
pca <- p$pan_pca()
summary(pca)
## ---- message=FALSE-----------------------------------------------------------
library(ggplot2)
library(patchwork) # To arrange plots
## -----------------------------------------------------------------------------
# Basic
pie1 <- p$gg_pie() + ggtitle("Default")
# Customize with ggplot2
pie2 <- pie1 +
ggtitle("Customized") +
theme_bw(base_size = 15) +
scale_fill_brewer(palette = "Blues")
# Arrange (patchwork) and plot
pie1 + pie2
## -----------------------------------------------------------------------------
p$gg_barplot()
## -----------------------------------------------------------------------------
p$gg_binmap()
## -----------------------------------------------------------------------------
p$gg_curves()
## ---- warning=FALSE-----------------------------------------------------------
p$gg_curves() +
ggtitle("Pangenome and Coregenome curves") +
geom_point() +
facet_wrap(~Category, scales = 'free_y') +
theme_bw(base_size = 15) +
scale_color_brewer(palette = "Accent")
## -----------------------------------------------------------------------------
p$organisms
## ---- warning=FALSE-----------------------------------------------------------
p$gg_pca(colour = 'host', size = 4) +
theme_bw(base_size = 15) +
scale_color_brewer(palette = "Set2")
## ---- eval=FALSE--------------------------------------------------------------
# p$runShinyApp()
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