我是 R 初学者,我正在尝试使用该包ClonEvol,但是 github 网页上的文档非常有限。所以现在我正在使用他们的示例代码并尝试将其适应我的数据,称为ce.
ce <- data.frame(
cluster = c(1,1,1,1,2,2,2,2,3,3,3,3,4,4,4,4,5,5,5,5,6,6,6,6,7,7,7,7),
gene = c("geneA","geneB","geneC","geneD","geneA","geneB","geneC","geneD","geneA","geneB","geneC","geneD","geneA","geneB","geneC",
"geneD","geneA","geneB","geneC","geneD","geneA","geneB","geneC","geneD","geneA","geneB","geneC","geneD"),
prim.vaf = c(0.5,0,0,0,0.5,0.5,0,0,1,0.5,0,0,1,0.5,0,0.5,0.5,0.5,0,0.5,0.5,0.5,0,1,0.5,0.5,0.5,0)
)
cluster <- ce$cluster
gene <- ce$gene
prim.vaf <- ce$prim.vaf
x <- ce
vaf.col.names <- grep('prim.vaf', colnames(x), value=T)
sample.names <- gsub('prim.vaf', '', vaf.col.names)
x[, sample.names] <- x[, vaf.col.names]
vaf.col.names <- sample.names
sample.groups <- c('P', 'R');
names(sample.groups) <- vaf.col.names
x <- x[order(x$cluster),]
pdf('box.pdf', width = 3, height = 5, useDingbats = FALSE, title='')
pp <- variant.box.plot(x,
cluster.col.name = ce$cluster,
show.cluster.size = FALSE,
cluster.size.text.color = 'blue',
vaf.col.names = vaf.col.names,
vaf.limits = 70,
sample.title.size = 20,
violin = FALSE,
box = FALSE,
jitter = TRUE,
jitter.shape = 1,
jitter.color = clone.colors,
jitter.size = 3,
jitter.alpha = 1,
jitter.center.method = 'median',
jitter.center.size = 1,
jitter.center.color = 'darkgray',
jitter.center.display.value = 'none',
highlight = 'is.driver',
highlight.note.col.name = 'gene',
highlight.note.size = 2,
highlight.shape =16,
order.by.total.vaf = FALSE
)
dev.off()
但是,我收到以下错误:
Error in .subset2(x, i, exact = exact) : recursive indexing failed at level 2
如果我删除cluster.col.name=ce$簇 and vaf.col.names=vaf.col.names,错误变为如下:
Error in .subset2(x, i, exact = exact) : attempt to select less than one
element in get1index
有人知道出了什么问题吗?