Hi!
Im learning to make heat maps.
I have used this data as a test:
http://llmpp.nih.gov/DLBCL/ called "Web Figure 1 Data file"
This is the code I used:
data <- read.table(file = "~/RNAseq/INFSTK-5010/Oblig1/NEJM_Web_Fig1data.txt", header = FALSE, skip = 1, sep = "\t")
dim(data)
test <- count.fields("~/RNAseq/INFSTK-5010/Oblig1/NEJM_Web_Fig1data.txt", sep="\t")
which(test != 295)
header = scan("~/RNAseq/INFSTK-5010/Oblig1/NEJM_Web_Fig1data.txt", "", n = 295)
colnames(data) = header
fixdata <- data[-7401,]
x <- data.matrix(fixdata[,-2], rownames.force = NA)
rownames(x) <- fixdata[,1]
x[is.na(x)] = 0
colclust <- hclust(as.dist(1-cor(x, method="pearson")), method="average")
rowclust <- hclust(as.dist(1-cor(t(x), method="pearson")), method="complete")
z <- x[rev(rowclust$labels[rowclust$order]), colclust$labels[colclust$order]]
plotHeatmap(z, fast = TRUE)
Plotting z:
Rplot2.pdf
Heatmap:
What has happened here?
Thanks!
Im learning to make heat maps.
I have used this data as a test:
http://llmpp.nih.gov/DLBCL/ called "Web Figure 1 Data file"
This is the code I used:
data <- read.table(file = "~/RNAseq/INFSTK-5010/Oblig1/NEJM_Web_Fig1data.txt", header = FALSE, skip = 1, sep = "\t")
dim(data)
test <- count.fields("~/RNAseq/INFSTK-5010/Oblig1/NEJM_Web_Fig1data.txt", sep="\t")
which(test != 295)
header = scan("~/RNAseq/INFSTK-5010/Oblig1/NEJM_Web_Fig1data.txt", "", n = 295)
colnames(data) = header
fixdata <- data[-7401,]
x <- data.matrix(fixdata[,-2], rownames.force = NA)
rownames(x) <- fixdata[,1]
x[is.na(x)] = 0
colclust <- hclust(as.dist(1-cor(x, method="pearson")), method="average")
rowclust <- hclust(as.dist(1-cor(t(x), method="pearson")), method="complete")
z <- x[rev(rowclust$labels[rowclust$order]), colclust$labels[colclust$order]]
plotHeatmap(z, fast = TRUE)
Plotting z:
Rplot2.pdf
Heatmap:
What has happened here?
Thanks!
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