利用R语言heatmap.2函数进行聚类并画热图

  
library(gplots)
data(mtcars)
x <- as.matrix(mtcars)
rc <- rainbow(nrow(x), start=0, end=.3)
cc <- rainbow(ncol(x), start=0, end=.3)

  
heatmap.2(x)

  
heatmap.2(x, dendrogram=“none”)

  
heatmap.2(x, dendrogram=“row”) # 只显示行向量的聚类情况
heatmap.2(x, dendrogram=“col”) #只显示列向量的聚类情况

  
heatmap.2(x, keysize=2) ## default - dendrogram plotted and reordering done.
heatmap.2(x, Rowv=FALSE, dendrogram=“both”) ## generate warning!
heatmap.2(x, Rowv=NULL, dendrogram=“both”) ## generate warning!
heatmap.2(x, Colv=FALSE, dendrogram=“both”) ## generate warning!

  
heatmap.2(x, srtCol=NULL)
heatmap.2(x, srtCol=0, adjCol = c(0.5,1) )
heatmap.2(x, srtCol=45, adjCol = c(1,1) )
heatmap.2(x, srtCol=135, adjCol = c(1,0) )
heatmap.2(x, srtCol=180, adjCol = c(0.5,0) )
heatmap.2(x, srtCol=225, adjCol = c(0,0) ) ## not very useful
heatmap.2(x, srtCol=270, adjCol = c(0,0.5) )
heatmap.2(x, srtCol=315, adjCol = c(0,1) )
heatmap.2(x, srtCol=360, adjCol = c(0.5,1) )

  
heatmap.2(x, srtRow=45, adjRow=c(0, 1) )
heatmap.2(x, srtRow=45, adjRow=c(0, 1), srtCol=45, adjCol=c(1,1) )
heatmap.2(x, srtRow=45, adjRow=c(0, 1), srtCol=270, adjCol=c(0,0.5) )

  
## Show effect of offsetRow/offsetCol (only works when srtRow/srtCol is 
## not also present) heatmap.2(x, offsetRow=0, offsetCol=0)
heatmap.2(x, offsetRow=1, offsetCol=1) 
heatmap.2(x, offsetRow=2, offsetCol=2) 
heatmap.2(x, offsetRow=-1, offsetCol=-1) 
heatmap.2(x, srtRow=0, srtCol=90, offsetRow=0, offsetCol=0)
heatmap.2(x, srtRow=0, srtCol=90, offsetRow=1, offsetCol=1)
heatmap.2(x, srtRow=0, srtCol=90, offsetRow=2, offsetCol=2)
heatmap.2(x, srtRow=0, srtCol=90, offsetRow=-1, offsetCol=-1)

  
## Show effect of z-score scaling within columns, blue-red color scale 
hv <- heatmap.2(x, col=bluered, scale=“column”, tracecol=“#303030”)

  
> names(hv) # 可以看到hv对象里面有很多子对象
> “rowInd” “colInd” “call” “colMeans” “colSDs” “carpet” “rowDendrogram” “colDendrogram” “breaks” “col” “vline” “colorTable” ## Show the mapping of z-score values to color bins hvKaTeX parse error: Expected 'EOF', got '#' at position 638: …an class="com">#̲# Extract the r…colorTable[hvKaTeX parse error: Expected 'EOF', got '#' at position 124: …n class="str">"#̲FFFFFF"</span><…colorTable[hvKaTeX parse error: Expected 'EOF', got '#' at position 124: …n class="str">"#̲FFFFFF"</span><…colSDs + hv$colMeans</span><spanclass="pun">,</span><spanclass="pln">whiteBin</span><spanclass="pun">[</span><spanclass="lit">2</span><spanclass="pun">]</span><spanclass="pln"></span><spanclass="pun">\ast </span><spanclass="pln">hv$colSDs + hvKaTeX parse error: Expected 'EOF', got '#' at position 1148: …n class="str">"#̲303030"</span><…Type)],
 xlab=‘CellLines’,
 ylab=‘Probes’,
 main=Cluster_Method[i],
 col=greenred(64))
 dev.off()
}

  
require(graphics)
hc <- hclust(dist(USArrests), “ave”)
plot(hc)