下三角相关热图

Question

我正试图在lower triangle中生成heatmap R成对关联。

以下是数据：

set.seed(1)
mat <- matrix(rnorm(6*10),ncol=6,nrow=10)
colnames(mat) <- c("s.-.+.1","s.-.+.2","s.-.+.3","s.+.-.1","s.+.-.2","s.+.-.3")

这是我正在尝试的代码：

getUpperTri <- function(cor.mat){
  cor.mat[lower.tri(cor.mat)] <- NA
  return(cor.mat)
}

reorderCormat <- function(cor.mat){
  dist.mat <- as.dist((1-cor.mat)/2)
  hc <- hclust(dist.mat)
  cor.mat <-cor.mat[hc$order,hc$order]
}
cor.df <- reshape2::melt(getUpperTri(reorderCormat(cor(mat))),na.rm=TRUE,value.name="correlation",varnames=c("sample1","sample2"))

ggplot heatmap代码为：

require(ggplot2)
ggplot(cor.mat.df,aes(sample2,sample1,fill=correlation))+geom_tile(color="white")+scale_fill_gradient2(low="blue",high="red",mid="white",midpoint=0,limit=c(-1,1),space="Lab",name="Pearson\nCorrelation")+theme_bw()+theme(axis.text.x=element_text(angle=45,vjust=1,size=10,hjust=1))+coord_fixed()+labs(x="",y="")

这给了我：

因此，有色元素遍布各处而不是局限于下三角。

知道问题是什么？

Answer 1

好吧，我复制了你的剧本，这是我的情节

只需更改

ggplot(cor.mat.df ,aes(sample2, sample1, fill=correlation))+
  geom_tile(color="white")+
  scale_fill_gradient2(low="blue", high="red", mid="white", midpoint=0, limit=c(-1,1), space="Lab", name="Pearson\nCorrelation")+
  theme_bw()+
  theme(axis.text.x=element_text(angle=45,vjust=1,size=10,hjust=1))+
  coord_fixed()+
  labs(x="",y="")

通过

ggplot(cor.df, aes(sample2, sample1, fill=correlation))+
  geom_tile(color="white")+
  scale_fill_gradient2(low="blue", high="red", mid="white", midpoint=0, limit=c(-1,1), space="Lab", name="Pearson\nCorrelation")+
  theme_bw()+
  theme(axis.text.x=element_text(angle=45, vjust=1, size=10, hjust=1))+
  coord_fixed()+
  labs(x="",y="")

我的sessionInfo：

R version 3.3.2 (2016-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=Spanish_Colombia.1252  LC_CTYPE=Spanish_Colombia.1252   
[3] LC_MONETARY=Spanish_Colombia.1252 LC_NUMERIC=C                     
[5] LC_TIME=Spanish_Colombia.1252    

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

other attached packages:
[1] ggplot2_2.2.1

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.8      digest_0.6.11    assertthat_0.1   grid_3.3.2       plyr_1.8.4      
 [6] gtable_0.2.0     magrittr_1.5     scales_0.4.1     stringi_1.1.2    reshape2_1.4.2  
[11] lazyeval_0.2.0   labeling_0.3     tools_3.3.2      stringr_1.1.0    munsell_0.4.3   
[16] colorspace_1.3-2 tibble_1.2