Question

我正在尝试在R中创建单倍型网络。我已经能够毫无问题地绘制它，但是尽管使用了scale.ratio值，但是在重叠节点方面存在一些问题。所以我想使用tkplot并手动进行我需要的更改，但是我没有运气介绍我在常规绘图函数下使用的饼图和大小值。

我对R很新，所以我希望我不知道自己在做什么，而不是尝试一些不可行的东西：）

提前感谢您的帮助！

这是我到目前为止的代码：

library(pegas)
library(plyr)
library(reshape)
library(igraph)

# Load the alignment
alignment<-read.dna("ON-A-SNP-data - Copy2.fas", format="fasta")

# Load the sites
sites<-read.csv("SITES.csv")

# Calculate haplotype frequencies
h<-haplotype(alignment)

# Build the haplotype network based on the haplotype frequencies.
net<-haploNet(h)

# Add column for haplotypes
sites<-cbind(sites,haplotype=rep(NA, nrow(sites)))

# Assign haplotypes to the samples automatically using a loop
for (i in 1:length(labels(h))){
    sites$haplotype[attr(h, "index")[[i]]]<-i
}

# Build a matrix of frequencies that will tell R how to fill pies on haplotype network.     #Requires    the packages 'plyr' and 'reshape'.
dfcount<-ddply(sites,.(site,haplotype),summarise,freq=length(site))
dc <- cast(haplotype ~ site, data = dfcount, value = "freq", fill = 0)
dc$haplotype<-NULL
dc<-as.matrix(as.data.frame(dc))

# Plot the haplotype network
plot(net, size=attr(net, "freq"), scale.ratio = 3, pie = dc, fast=TRUE, labels=FALSE)

如果这有用，这是'net'的输出？

> net
            step      Prob
 [1,] 10  9    1 0.9939576
 [2,] 13 12    1 0.9939576
 [3,] 14 12    1 0.9939576
 [4,] 15 14    1 0.9939576
 [5,] 16 14    1 0.9939576
 [6,] 17 14    1 0.9939576
 [7,] 18 14    1 0.9939576
 [8,] 30 29    1 0.9939576
 [9,] 31 29    1 0.9939576
[10,] 32 29    1 0.9939576
[11,] 11  9    2 0.9819270
[12,] 19 14    2 0.9819270
[13,] 20 14    2 0.9819270
[14,] 21 14    2 0.9819270
[15,] 22 14    2 0.9819270
[16,] 23 14    2 0.9819270
[17,] 24 14    2 0.9819270
[18,] 25 14    2 0.9819270
[19,] 12  7    3 0.9640739
[20,] 12  9    3 0.9640739
[21,] 34 12    3 0.9640739
[22,] 26 14    3 0.9640739
[23,]  8  7    4 0.9406588
[24,] 29 12    4 0.9406588
[25,] 27 14    4 0.9406588
[26,] 28 14    4 0.9406588
[27,] 33 29    4 0.9406588
[28,]  7  1    5 0.9120671
[29,]  7  2    5 0.9120671
[30,]  5  4    5 0.9120671
[31,]  7  3    6 0.8787358
[32,]  7  4    7 0.8412104
[33,]  7  6    9 0.7560227
attr(,"freq")
 [1] 1 1 1 1 1 3 1 1 3 1 1 3 1 9 2 1 1 1 1 1 1 1 1 1 1 1 1 1 7 1 1 1 1 1
attr(,"labels")
 [1] "I"      "II"     "III"    "IV"     "V"      "VI"     "VII"    "VIII"   "IX"     "X"     
[11] "XI"     "XII"    "XIII"   "XIV"    "XV"     "XVI"    "XVII"   "XVIII"  "XIX"    "XX"    
[21] "XXI"    "XXII"   "XXIII"  "XXIV"   "XXV"    "XXVI"   "XXVII"  "XXVIII" "XXIX"   "XXX"   
[31] "XXXI"   "XXXII"  "XXXIII" "XXXIV" 
attr(,"class")
[1] "haploNet"

R haploNet with tkplot（igraph）

0 个答案: