如何使用xyz异类数据在R中制作热图

Lib*_*oja 3 r graph gnuplot heatmap

我正在尝试在R建议中使用A真正的热图,但是出现错误:

interp.old(x,y,z,xo = xo,yo = yo,ncp = 0,extrap = extrap,
:x和y的比例太不同了

在代码行之后:

 s <- interp(x,y,z)
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我的数据被构造为期望在深色连续背景中获得彩色的热图,如线条,并且可以GNUplot使用set pm3d map和来工作set hidden3d。数据对应y于给定时间(x)中分子产生()的模型,其出现频率用表示z。看起来像这样:

1.000000000000e+00  1e-8    0

1.000000000000e+00  5e-8    0

1.000000000000e+00  1e-7    5

1.000000000000e+00  5e-7    0

1.000000000000e+00  1e-6    0

1.000000000000e+00  5e-6    0

1.000000000000e+00  1e-5    0

1.000000000000e+00  5e-5    0

1.000000000000e+00  1e-4    0

1.000000000000e+00  5e-4    0

1.000000000000e+00  1e-3    0

1.000000000000e+00  5e-3    0

1.000000000000e+00  1e-2    0

1.000000000000e+00  5e-2    0

1.000000000000e+00  1e-1    0

1.000000000000e+00  5e-1    0

1.000000000000e+00  1e+1    0

1.000000000000e+00  5e+1    0

1.000000000000e+00  1e+2    0

1.000000000000e+00  5e+2    0

1.000000000000e+00  1e+3    0

1.000000000000e+00  5e+3    0

1.000000000000e+00  1e+4    0

1.000000000000e+00  5e+4    0

1.000000000000e+00  1e+5    0

1.000000000000e+00  5e+5    0

1.000000000000e+00  1e+6    0

1.000000000000e+00  5e+6    0

1.000000000000e+00  1e+7    0

1.000000000000e+00  5e+7    0

1.000000000000e+00  1e+8    0

1.000000000000e+00  5e+8    0

2.000000000000e+00  1e-8    0

2.000000000000e+00  5e-8    0

2.000000000000e+00  1e-7    0

2.000000000000e+00  5e-7    5

2.000000000000e+00  1e-6    0

2.000000000000e+00  5e-6    0

2.000000000000e+00  1e-5    0

2.000000000000e+00  5e-5    0

2.000000000000e+00  1e-4    0

2.000000000000e+00  5e-4    0

2.000000000000e+00  1e-3    0

2.000000000000e+00  5e-3    0

2.000000000000e+00  1e-2    0

2.000000000000e+00  5e-2    0

2.000000000000e+00  1e-1    0

2.000000000000e+00  5e-1    0

2.000000000000e+00  1e+1    0

2.000000000000e+00  5e+1    0

2.000000000000e+00  1e+2    0

2.000000000000e+00  5e+2    0

2.000000000000e+00  1e+3    0

2.000000000000e+00  5e+3    0

2.000000000000e+00  1e+4    0

2.000000000000e+00  5e+4    0

2.000000000000e+00  1e+5    0

2.000000000000e+00  5e+5    0

2.000000000000e+00  1e+6    0

2.000000000000e+00  5e+6    0

2.000000000000e+00  1e+7    0

2.000000000000e+00  5e+7    0

2.000000000000e+00  1e+8    0

2.000000000000e+00  5e+8    0

3.000000000000e+00  1e-8    0

3.000000000000e+00  5e-8    0

3.000000000000e+00  1e-7    0

3.000000000000e+00  5e-7    0

3.000000000000e+00  1e-6    5

3.000000000000e+00  5e-6    0

3.000000000000e+00  1e-5    0

3.000000000000e+00  5e-5    0

3.000000000000e+00  1e-4    0

3.000000000000e+00  5e-4    0

3.000000000000e+00  1e-3    0

3.000000000000e+00  5e-3    0

3.000000000000e+00  1e-2    0

3.000000000000e+00  5e-2    0

3.000000000000e+00  1e-1    0

3.000000000000e+00  5e-1    0

3.000000000000e+00  1e+1    0

3.000000000000e+00  5e+1    0

3.000000000000e+00  1e+2    0

3.000000000000e+00  5e+2    0

3.000000000000e+00  1e+3    0

3.000000000000e+00  5e+3    0

3.000000000000e+00  1e+4    0

3.000000000000e+00  5e+4    0

3.000000000000e+00  1e+5    0

3.000000000000e+00  5e+5    0

3.000000000000e+00  1e+6    0

3.000000000000e+00  5e+6    0

3.000000000000e+00  1e+7    0

3.000000000000e+00  5e+7    0

3.000000000000e+00  1e+8    0

3.000000000000e+00  5e+8    0

4.000000000000e+00  1e-8    0

4.000000000000e+00  5e-8    0

4.000000000000e+00  1e-7    0

4.000000000000e+00  5e-7    0

4.000000000000e+00  1e-6    0

4.000000000000e+00  5e-6    5

4.000000000000e+00  1e-5    0

4.000000000000e+00  5e-5    0

4.000000000000e+00  1e-4    0

4.000000000000e+00  5e-4    0

4.000000000000e+00  1e-3    0

4.000000000000e+00  5e-3    0

4.000000000000e+00  1e-2    0

4.000000000000e+00  5e-2    0

4.000000000000e+00  1e-1    0

4.000000000000e+00  5e-1    0

4.000000000000e+00  1e+1    0

4.000000000000e+00  5e+1    0

4.000000000000e+00  1e+2    0

4.000000000000e+00  5e+2    0

4.000000000000e+00  1e+3    0

4.000000000000e+00  5e+3    0

4.000000000000e+00  1e+4    0

4.000000000000e+00  5e+4    0

4.000000000000e+00  1e+5    0

4.000000000000e+00  5e+5    0

4.000000000000e+00  1e+6    0

4.000000000000e+00  5e+6    0

4.000000000000e+00  1e+7    0

4.000000000000e+00  5e+7    0

4.000000000000e+00  1e+8    0

4.000000000000e+00  5e+8    0
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第一个建议给了我一些丑陋的结果,类似于最初在R中的A真热图中获得的结果,该是由一些水平线组成的图,其中水平线充满了不同的灰度色调。第二个似乎崩溃了。我从中收到此消息:

>Traceback:
1: .Fortran("idsfft", as.integer(1), as.integer(ncp), as.integer(n),     as.double(x),  as.double(y), as.double(z), as.integer(nx),     as.integer(ny), x = as.double(xo), y = as.double(yo), z = zo,     integer((31 + ncp) * n + nx * ny), double(5 * n), misso = as.logical(misso),     PACKAGE = "akima")
2: interp.old(x, y, z, xo = xo, yo = yo, ncp = 0, extrap = extrap,     duplicate = duplicate, dupfun = dupfun)
3: interp(x, y, z)

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
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我只是添加了更多数据,以防它有所帮助。我这样称呼数据框中的列:

coso <-read.table(“ / home / libertad / mygraphs / two / two_1_90 / coso.txt”,标头= FALSE,sep =“ \ t”)

>x <-coso[[1]]

>y <-coso[[2]]
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这是我在GNUplot中使用的图形之一,我希望使用R可以得到更好的图形。

gau*_*den 5

建议的解决方案

使用scale()变换x和y可比尺度。

模拟

fields按照您的问题使用软件包:

library(akima) 
library(fields) 

x <- rnorm(20, 4, 3)
y <- rnorm(20, 5e-5, 1e-5)
x <- scale(x) # comment out these two lines 
y <- scale(y) # to reproduce your error
z <- rnorm(20)

s <- interp(x,y,z)
image.plot(s)
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使用ggplot2,改编自我的其他答案

library(akima) 
library(ggplot2) 

x <- rnorm(20, 4, 3)
y <- rnorm(20, 5e-5, 1e-5)
x <- scale(x) # comment out these two lines 
y <- scale(y) # to reproduce your error
z <- rnorm(20)

t. <- interp(x,y,z)
t.df <- data.frame(t.)

gt <- data.frame( expand.grid(X1=t.$x, 
                              X2=t.$y), 
                  z=c(t.$z), 
                  value=cut(c(t.$z), 
                            breaks=seq(min(z),max(z),0.25)))

p <- ggplot(gt) + 
    geom_tile(aes(X1,X2,fill=value)) + 
    geom_contour(aes(x=X1,y=X2,z=z), colour="black") 
p
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校正轴标签

在另一个问题中,还描述了在重新缩放之前用原始数据的正确值标记轴的解决方案。目前仅适用于ggplot