## ----echo=FALSE, results="hide", warning=FALSE--------------------------------
suppressPackageStartupMessages({library('MSTree')})

## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>"
)

## ----eval=TRUE----------------------------------------------------------------
cgmlst_output <- system.file("extdata", "cgMLST95.csv", package = "MSTree")

my_graph <- makeGraphFromChewBBACA(cgmlst_output, max_allelic_difference = 9)

mst <- PlotMST(my_graph, show_clustering = TRUE, show_legend=FALSE, 
    MST_edges_color="#b97b29", node_color = "#3b17db", 
    node_label_size = 3, title = "MST")

mst

## -----------------------------------------------------------------------------
sessionInfo()