2014-03-11

x <- scale(x, center = FALSE)

hmap(x, labRow = FALSE, method = "OLO")

hmap(x, labRow = FALSE, method = "OLO", col=diverge_hcl(100), range=c(-3.5,3.5), colorkey=TRUE)


hmap(x, labRow = FALSE, method = "OLO", col = c("yellow", "blue"))

x <- read.csv(file="/Bioinformatics/Users/zfu/2014_BP_TB_Paper/rank_log2.csv", head=TRUE,sep=",")
x
attributes(x)
x <- as.matrix(x)
x
attributes(x)
x[1:10,]
?read.csv
x <- read.table(file="/Bioinformatics/Users/zfu/2014_BP_TB_Paper/rank_log2.csv", head=TRUE, sep=",", row.names=1)
x
x <- data.matrix(x)
x
attributes(x)
x[1:10,]
library(seritation)
library(seriation)
o <- c(seriate(dist(x), method ="OLO"),seriate(dist(t(x)), method = "OLO"))
o
history
history(100)

o1 <- seriate(dist(x), method = "OLO")
o2 <- seriate(dist(t(x)), method = "OLO")
o1
desribe(o1)
attributes(o1)
attributes(o2)
o1[1]
o1[[1]]
o1[[1]][1]
o1[[1]][[1]]
attributes(o1[[1]][[1]])
head(get_order(o1))
order1 <- get_order(o1)
order2 <- get_order(o2)
order2
x
attributes(x)
clustered_data <- x[order1,order2]
clustered_data
clustered_data[1:2,]
ls()
history(100)
> pdf("aa.pdf")
> heatmap.2(clustered_data, col=my_palette, scale="none", Colv = NULL, dendrogram = "row", key=T, keysize = 1.5, density.info="none", trace="none",cexCol=0.9, labRow=NA)
> dev.off()
null device
          1
> heatmap.2(clustered_data, col=my_palette, scale="none", dendrogram = "column", key=T, keysize=1.5, density.info="none", trace="none",cexCol=0.5, labRow=NA)


cc = c(rep("blue",10),rep("brown",11),rep("cyan",11),rep("orange",4),rep("red",15))


heatmap.2(scale(x1), col=my_palette, scale="none", Colv=NULL, dendrogram = "row", density.info="none", trace="none", cexCol=0.3, labRow=NA, labCol=NA, margin=c(12, 12), key=T, keysize=1)


aa_disease
pdf("/Bioinformatics/Users/zfu/2014_BP_TB_Paper/figure3_diseaseType.pdf")
heatmap.2(clustered_data, col=my_palette, scale="none", dendrogram = "column", key=T, keysize=1, density.info="none", trace="none",cexCol=0.3, labRow=NA, ColSideColors=aa_disease, margin=c(12, 12), labCol=NA)
dev.off()
aa_disease
colnames(clustered_data)
pdf("/Bioinformatics/Users/zfu/2014_BP_TB_Paper/test.pdf")
heatmap.2(clustered_data, col=my_palette, scale="none", dendrogram = "column", key=T, keysize=1, density.info="none", trace="none",cexCol=0.3, labRow=NA, ColSideColors=aa_disease, margin=c(12, 12))
dev.off()
x1 <- read.table(file="/Bioinformatics/Users/zfu/2014_BP_TB_Paper/th1_th17_signiture.csv", head=TRUE, sep=",", row.names=1)
x1 <- as.matrix(x1)
attributes9x1)
attributes(x1)
pdf("/Bioinformatics/Users/zfu/2014_BP_TB_Paper/Th1_Th17_Significant.pdf")
heatmap.2(scale(x1), col=my_palette, scale="none", Colv=NULL, dendrogram = "row", density.info="none", trace="none", cexCol=0.3, labRow=NA, labCol=NA, margin=c(12, 12))
dev.off()
pdf("/Bioinformatics/Users/zfu/2014_BP_TB_Paper/Th1_Th17_Significant.pdf")
x1
scale(x1)
heatmap.2(scale(x1), col=my_palette, scale="none", Colv=NULL, dendrogram = "row", density.info="none", trace="none", cexCol=0.3, labRow=NA, labCol=NA, margin=c(12, 12), key=T, keysize=1)
dev.off()
history(-25)
history(25)






x1 <- read.table(file="/Bioinformatics/Users/zfu/2014_BP_TB_Paper/th1_th17_signiture_data.csv", head=TRUE, sep=",", row.names=1)
x1 <- as.matrix(x1)
pdf("/Bioinformatics/Users/zfu/2014_BP_TB_Paper/Th1_Th17_Significant.pdf")
heatmap.2(scale(x1), col=my_palette, scale="none", Colv=NULL, dendrogram = "row", density.info="none", trace="none", cexCol=0.3, labRow=NA, labCol=NA, margin=c(12, 12))
dev.off()
pdf("/Bioinformatics/Users/zfu/2014_BP_TB_Paper/Th1_Th17_Significant.pdf")
heatmap.2(scale(x1), col=my_palette, scale="none", Colv=NULL, dendrogram = "none", density.info="none", trace="none", cexCol=0.3, labRow=NA, labCol=NA, margin=c(12, 12))
dev.off()
pdf("/Bioinformatics/Users/zfu/2014_BP_TB_Paper/Th1_Th17_Significant.pdf")
heatmap.2(scale(x1), col=my_palette, scale="none", Colv=NULL, dendrogram = "none", density.info="none", trace="none", cexCol=0.3, labRow=NA, margin=c(12, 12))
dev.off()
pdf("/Bioinformatics/Users/zfu/2014_BP_TB_Paper/Th1_Th17_Significant.pdf")
heatmap.2(scale(x1), col=my_palette, scale="none", Colv=NULL, dendrogram = "none", density.info="none", trace="none", cexCol=0.3, labRow=NA, margin=c(12, 12), labCol=NA)