如何与X轴从-X到X中的R

问题描述：

我有一个看起来像这样的数据帧绘制：如何与X轴从-X到X中的R

> dataf 
     gene_name   log.pval    log.fc 
1   TNIP3 0.631094308480128 1.1506542453426 
2 NP_808217.1 0.772551410812959 -0.808513121902601 
3 Q6ZQS7_HUMAN 0.120675567248996 1.20907596997608 
4 Q8TA88_HUMAN 1.44494939509263 2.06552619626619 
5   THAP5 0.766534371246673 1.13887517622511 
6  BHLHB5 0.596510549476608 -0.890552737707591 
7 XP_372337.2 0.495557665215951 -0.896828380212937 
8 Q7Z2R7_HUMAN 0.448309045489994 -1.81608512967947 
9  IFITM2 0.453896048090579 1.63881366592662 
10   - 1.28765417650748 -0.95944121604072

我想要做的是使用具有与x轴的曲线图log.fc列和使用log.pval列的y轴。

但为什么这个命令失败？

plot(dataf$log.fc,dataf$log.pval,xlim=c(-2,2),ylim=c(0,5));

它给了我下面的错误信息：

Error in if (equidist) seq.int(1/(2 * ny), 1 - 1/(2 * ny), by = 1/ny) else (yat[-1L] + : 
    missing value where TRUE/FALSE needed 
Calls: plot -> plot.factor -> spineplot -> spineplot.default 
In addition: Warning messages: 
1: In spineplot.default(x, y, ...) : 
    x axis is on a cumulative probability scale, 'xlim' must be in [0,1] 
2: In spineplot.default(x, y, ...) : 
    y axis is on a cumulative probability scale, 'ylim' must be in [0,1] 
Execution halted

更新：输入数据和完整的代码。

输入文件mydata.csv：

Name|ID_REF|xN|xK|xD|yN|yK|yD 
NP_542387.1|H200009573|116.344280521|157.34028943|165.521765927|129.382514146|146.734212992|111.564081171 
TRIM65|H200014442|139.28243473|142.8535596|183.543914333|151.18230485|126.012002369|117.926240275 
Q96JT4_HUMAN|H200011360|6.30624488407|6.23249632016|8.84048629421|3.67264474301|1.78051470938|3.00185438056 
MTCH1|H200017563|962.796774907|984.466886282|1225.05018099|1006.35251622|959.451292287|1004.59648311 
RPL35|H200008624|13462.3246704|16392.4312316|16124.489617|15544.2347278|16130.3829312|12319.5940351

代码：

data<-read.delim("~/Desktop/mydata.csv",sep="|",na.strings="",header=TRUE,blank.lines.skip=TRUE,fill=FALSE) 
data<- data[complete.cases(data),] 

gname <- as.matrix(data$Name); 
idref <- as.matrix(data$ID_REF); 
xN <- data$xN; 
xK <- data$xK; 
xD <- data$xD; 
yN <- data$yN; 
yK <- data$yK; 
yD <- data$yD; 


xK_yK <- as.matrix(cbind(xK,yK)); 
xD_yD <- as.matrix(cbind(xD,yD)); 
xN_yN <- as.matrix(cbind(xN,yN)); 


#-------------------------------------------------- 
# Functions 
#-------------------------------------------------- 
foldchange_geom_avg <- function(r,g) { 
    # r and g is vector with value >=1 
    # Essentially the same with M value 
    # >0 if r is upregulated 
    # <0 if r is downregulated 
    return (sum(log2(r/g))/length(r)); 
} 


ranked.ttest <- function(gn,v1,v2,test.type="t") { 
     # By default t.test assume unequal variance 
     # and applies Welsh modification 
     # These samples are assumed also to be independent 
     # and the distributions are strictly normal 

     # Mann-Whitney (Wilcoxon) assume no-normality 
     # and with arbitrary sample 

     out <- c(); 

     for (i in 1:nrow(v1)) { 

      test <- t.test(v1[i,],v2[i,],paired=FALSE) 

      if (test.type == "mw") { 
       test <- wilcox.test(v1[i,],v2[i,],alternative="two.sided",paired=FALSE) 
      } 

      pval <- test$p.value; 
      log.pval <- -log10(pval); 
      gene_name <- gn[i]; 
      log.fc <- foldchange_geom_avg(v1[i,],v2[i,]); 

      abs.fc <- abs(log.fc) 

      if (is.numeric(pval)){ 
       out <- rbind(out,cbind(gene_name,log.pval,pval,log.fc)); 
      } 
     } 
    #out <- out[with(out,order(pvalue,genename))] 
    return (data.frame(out)); 
} 



test <- ranked.ttest(gname,xK_yK,xN_yN) 
plot(test$log.fc,test$log.pval,xlim=c(-2,2),ylim=c(0,5));

这是会话信息：

> sessionInfo() 
R version 2.15.2 (2012-10-26) 
Platform: i386-apple-darwin9.8.0/i386 (32-bit) 

locale: 
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 

attached base packages: 
[1] stats  graphics grDevices utils  datasets methods base

和剧情是这样的： enter image description here

错误信息似乎完全信息。你已经创建了一个带有一个spineplot类的数据对象（或者其他类），并且plot方法并不期待负值。现在，为什么不用包名显示完整的代码？嗯？ – 2013-02-21 07:47:18

显示情节告诉我们什么都没有。我们需要看看数据对象是如何创建的。 – 2013-02-21 08:27:20

@DWin：我现在更新了完整的代码。 – neversaint 2013-02-21 08:48:07

答

您能否包括您的会话信息？当我运行代码时，我得到了不同的东西。

dataset<- textConnection("gene_name log.pval log.fc 
TNIP3 0.631094308480128 1.1506542453426 
NP_808217.1 0.772551410812959 -0.808513121902601 
Q6ZQS7_HUMAN 0.120675567248996 1.20907596997608 
Q8TA88_HUMAN 1.44494939509263 2.06552619626619 
THAP5 0.766534371246673 1.13887517622511 
BHLHB5 0.596510549476608 -0.890552737707591 
XP_372337.2 0.495557665215951 -0.896828380212937 
Q7Z2R7_HUMAN 0.448309045489994 -1.81608512967947 
IFITM2 0.453896048090579 1.63881366592662 
NA 1.28765417650748 -0.95944121604072") 

dataf <- read.table(dataset,header=TRUE) 

plot(dataf$log.fc,dataf$log.pval,xlim=c(-2,2),ylim=c(0,5))

enter image description here

谢谢。我更新了完整的代码。 – neversaint 2013-02-21 08:47:51

如何与X轴从-X到X中的R

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