如何在 R 中绘制剖面图? [英] How do I draw a profile plot in R?

问题描述

我想为不同时间点的 VPs8 基因生成轮廓图.

I want to generate a profile plot for VPs8 gene across different time points.

dat <- read.table("xyz", header=T, row.names=1)
cdc15 <- select(dat, 23:46)
VPS8 <- cdc15["YAL002W",]
VPS8_num <- data.frame(as.numeric(VPS8))

    names(VPS8) <- str_remove(names(VPS8), 'cdc15_')
plot(c(1, ncol(VPS8), range(na.omit(as.numeric(VPS8[1,]))), 
       type="n", xlab="", 
       ylab="log2(intensity)", 
       main="VPS8 expression in yeast S. cerevisiae 
       cdc15 mutant during different time points of cell cycle arrest", 
       axes=FALSE
       ))
lines(c(1:ncol(dat)), as.numeric(dat[VPs8]), lwd=2, col="blue")
grid()
axis(1, at=c(1:ncol(dat)), dimnames(dat)[[2]], las=2, cex.lab=0.7)
axis(2)

数据:

> dput(VPS8)
structure(list(cdc15_10 = NA_real_, cdc15_30 = NA_real_, cdc15_50 = NA_real_, 
    cdc15_70 = -0.58, cdc15_80 = 0.23, cdc15_90 = -0.23, cdc15_100 = 0.08, 
    cdc15_110 = -0.62, cdc15_120 = 0.55, cdc15_130 = -0.32, cdc15_140 = 0.03, 
    cdc15_150 = -0.56, cdc15_160 = 0.47, cdc15_170 = -0.15, cdc15_180 = 0.49, 
    cdc15_190 = NA_real_, cdc15_200 = 0.23, cdc15_210 = -0.49, 
    cdc15_220 = 0.33, cdc15_230 = 0.18, cdc15_240 = 0.65, cdc15_250 = -0.29, 
    cdc15_270 = NA_real_, cdc15_290 = NA_real_), row.names = "YAL002W", class = "data.frame")

CDC15

预期输出:生成 VPS8 基因的轮廓图.在 x 轴上，仅提供没有cdc15_"的时间点.前缀.

Desired output: Generate a profile plot for VPS8 gene. On the x-axis, provide only the time points without the "cdc15_" prefix.

错误:xj[i] 中的错误:无效的下标类型列表"

Error: Error in xj[i] : invalid subscript type 'list'

推荐答案

行

match <- str_remove(as.list(VPS8), "cdc15_")

没有意义.纯属偶然，它不会引发错误，但它没有任何用处.实际上，您似乎想从表的列名中删除cdc15_.你需要在这里做一些不同的事情:

makes no sense. By pure accident it doesn’t raise an error, but it does nothing useful. In reality, you seem to want to remove cdc15_ from the column names of your table. You’ll need to do something different here:

names(VPS8) <- str_remove(names(VPS8), 'cdc15_')

接下来，您观察到的实际错误来自于此:

Next, the actual error you’re observing is from this:

dat[VPS8,])

您正在使用 data.frame 作为子集的索引 - 这不受支持，并且不清楚您打算做什么.但根据数据，我猜该行应该如下所示(格式正确):

You are using a data.frame as an index for subsetting — this isn’t supported, and it isn’t clear what you intended to do. But based on the data I guess the line should probably look as follows (properly formatted):

plot(
    c(1, ncol(VPS8)),
    range(na.omit(as.numeric(VPS8[1, ]))),
    type = "n", xlab = "", 
    ylab = "log2(intensity)",
    main = "VPS8 expression in yeast S. cerevisiae cdc15 mutant during different time points of cell cycle arrest",
    axes = FALSE,
    lwd = 1
)

——当然，这纯粹是我的猜测，因为这没有绘制任何内容(因为你已经指定了 type = "n").

— Of course this is pure guesswork on my part, since this plots nothing (since you’ve specified type = "n").

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