對ggplot2中的特定數據執行統計測試

Question

我寫了一個使用ggplot2生成圖的腳本，並且在每個圖中都有多個x軸值，並且它們中的每一個在y軸上有多個值，這個軸。我將以另一種方式提出問題：我有一個數據框中的多個子集，在for循環中生成，我如何控制for的循環以便生成另一個包含在每個數據框中的數據框行（以前的數據幀的第一列的值）

for (x in phy) { 
    print(x) 

    test<-subset(t, Phylum==x) 
    dat <- melt(test, measure=c("A","C","G","T","(A-T)/(A+T)","(G-C)/(G+T)", 
           "(A+T)/(G+C)")) 
    unitest <- unique(c(test$Class)) 
    #print(nrow(test)) 
    i <- 1 
    for(y in unitest) { 
     towork <- subset(test, Class==y) 

     # here i want to create a data frame that will contain (in each row, the 
     # value of the first column of the towork subset for each y) 

     # atest=wilcox.test(towork$A,towork$A, correct=FALSE) 
     # print(paste(paste(y,towork$A),towork$A)) 
    } 
} 



input: 

    e.g 
    class1: 
    0.268912 0.158921 0.214082 0.358085 
    1.680946   0.314681 0.210526 0.166895 
    0.286945 0.322006 0.147361 0.243688 
    class2 
    0.293873 0.327516 0.156235 0.222376  
    0.327430 0.308667 0.135710 0.227695  
    0.301488 0.326511 0.125865 0.246022  
    0.310980 0.308730 0.148861 0.231429 

我想新的數據幀在每一行中包含每個類的第一列。

output 
    e.g 
    1st row: 0.268912 1.680946 0.286945 
    2nd row:0.293873 0.327430 0.301488 0.310980 

等... ，然後包含在每個其他數據幀的行的每個類 等的第2列...

比我想在每2行的執行統計測試新的數據框架（例如Wilcoxon Rank Sum Test）並獲得結果。

任何幫助將提前意識到

Hello , i came up with an idea , but i need your help to do it. 
first the data is in a large text file and i will upload it if you want , my idea is : create a function that take 2 argument : 
1.the name of the column which should be used for grouping the data (e.g. phylum, or class) 
2. the name of the column containing the data to test (e.g. A,C,G,T) 
and i will test the data for each phylum first , and if i want i will test it for each class in each phylum. 
that's mean,i will take the A column for first phylum and A column for 2nd phylum and make the wilcox.test on them , and i will make the process for each common column in each phylum. and then i will use a subset function to test the classes inside each phylum. 
give me your opininon with this ?? 

日Thnx。

Answer 1

我認爲這會做你以後的事情。我們不一定需要完成爲感興趣的四個變量創建新數據框架的過程 - 我們可以從class1和class2之內的各自位置提取感興趣的列。代碼已更新以查找class1和class2之間的公共列。它只會計算那些常見列的wilcox測試。

class1 <- matrix(rnorm(12), ncol = 4) 
class2 <- matrix(rnorm(16), ncol = 4) 

computeWilcox <- function(x, y, correct = FALSE, ...) { 

    if (!is.numeric(x)) stop("x must be numeric.") 
    if (!is.numeric(y)) stop("y must be numeric.") 

    commonCols <- intersect(colnames(x), colnames(y)) 

    ret <- vector("list", length(commonCols)) 

    for (col in 1:length(commonCols)) { 
     ret[[col]] <- wilcox.test(x[, col], y[, col], correct = correct, ...) 
    } 

    names(ret) <- commonCols 
    return(ret) 
} 


zz <- computeWilcox(class1, class2) 

其中ZZ具有如下的結構：

> str(zz) 
List of 2 
$ c:List of 7 
    ..$ statistic : Named num 0 
    .. ..- attr(*, "names")= chr "W" 
    ..$ parameter : NULL 
    ..$ p.value : num 0.0571 
    ..$ null.value : Named num 0 
    .. ..- attr(*, "names")= chr "location shift" 
    ..$ alternative: chr "two.sided" 
    ..$ method  : chr "Wilcoxon rank sum test" 
    ..$ data.name : chr "x[, col] and y[, col]" 
    ..- attr(*, "class")= chr "htest" 
$ d:List of 7 
    ..$ statistic : Named num 2 
    .. ..- attr(*, "names")= chr "W" 
    ..$ parameter : NULL 
    ..$ p.value : num 0.229 
    ..$ null.value : Named num 0 
    .. ..- attr(*, "names")= chr "location shift" 
    ..$ alternative: chr "two.sided" 
    ..$ method  : chr "Wilcoxon rank sum test" 
    ..$ data.name : chr "x[, col] and y[, col]" 
    ..- attr(*, "class")= chr "htest" 

您可以提取參數或p值出返回列表對象是這樣的：

> zz$c$p.value 
[1] 0.05714286