to repeat the example in the ClonEvol Tutorial by RGui4.0.2

[nypeterju]

First time User. Step by step to run the code in Tutorial by Dr. Dang, but some errors always come up. Need help! Thanks in advance.

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library(clonevol) library(devtools) Loading required package: usethis

data(aml1) x <- aml1$variants

#shorten vaf column names as they will be vaf.col.names <- grep('.vaf', colnames(x), value=T) sample.names <- gsub('.vaf', '', vaf.col.names) x[, sample.names] <- x[, vaf.col.names] vaf.col.names <- sample.names

prepare sample grouping

sample.groups <- c('P', 'R'); names(sample.groups) <- vaf.col.names

setup the order of clusters to display in various plots (later)

x <- x[order(x$cluster),]

clone.colors <- c('#999793', '#8d4891', '#f8e356', '#fe9536', '#d7352e')

pdf('box.pdf', width = 3, height = 3, useDingbats = FALSE, title='') pp <- plot.variant.clusters(x,

• cluster.col.name = 'cluster',
• show.cluster.size = FALSE,
• cluster.size.text.color = 'blue',
• vaf.col.names = vaf.col.names,
• vaf.limits = 70,
• sample.title.size = 20,
• violin = FALSE,
• box = FALSE,
• jitter = TRUE,
• jitter.shape = 1,
• jitter.color = clone.colors,
• jitter.size = 3,
• jitter.alpha = 1,
• jitter.center.method = 'median',
• jitter.center.size = 1,
• jitter.center.color = 'darkgray',
• jitter.center.display.value = 'none',
• highlight = 'is.driver',
• highlight.shape = 21,
• highlight.color = 'blue',
• highlight.fill.color = 'green',
• highlight.note.col.name = 'gene',
• highlight.note.size = 2,
• order.by.total.vaf = FALSE) Warning messages: 1: fun.y is deprecated. Use fun instead. 2: show_guide has been deprecated. Please use show.legend instead. 3: fun.y is deprecated. Use fun instead. 4: show_guide has been deprecated. Please use show.legend instead.

dev.off() null device 1