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hdng / clonevol

Inferring and visualizing clonal evolution in multi-sample cancer sequencing
GNU General Public License v3.0
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to repeat the example in the ClonEvol Tutorial by RGui4.0.2 #44

Open nypeterju opened 3 years ago

nypeterju commented 3 years ago

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.

R version 4.0.2 (2020-06-22) -- "Taking Off Again" Copyright (C) 2020 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit)

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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