#10 tested 4.0.4 image

R_workshop.2.Rmd

@@ -543,24 +543,19 @@ hist(log2(mean.after), breaks = H1$breaks, col = '#20502050', add = TRUE)
 Heatmaps are another regular plot to describe expression data among many other applications.  
 We will use the data and code from this webpage: https://davetang.org/muse/2018/05/15/making-a-heatmap-in-r-with-the-pheatmap-package/
 
-```{r, eval = F, echo = TRUE}
-if (!requireNamespace("BiocManager", quietly = TRUE))
-     install.packages("BiocManager", repos='http://cran.us.r-project.org' , 
-                      dependencies = TRUE, version = "1.30.10")
-BiocManager::install("DESeq")
-```
-
-```{r eval = T, message=FALSE, eval = FALSE}
+```{r, message=FALSE, eval = TRUE}
 library(pheatmap)
-library(DESeq)
 
-# load data and subset
-example_file = system.file ("extra/TagSeqExample.tab", package="DESeq")
-data = read.delim(example_file, header=T, row.names="gene")
-data_subset = as.matrix(data[rowSums(data)>50000,])
- 
-# create heatmap using pheatmap
-pheatmap(data_subset)
+# Generate some data
+test = matrix(rnorm(200), 20, 10)
+test[1:10, seq(1, 10, 2)] = test[1:10, seq(1, 10, 2)] + 3
+test[11:20, seq(2, 10, 2)] = test[11:20, seq(2, 10, 2)] + 2
+test[15:20, seq(2, 10, 2)] = test[15:20, seq(2, 10, 2)] + 4
+colnames(test) = paste("Test", 1:10, sep = "")
+rownames(test) = paste("Gene", 1:20, sep = "")
+
+# Draw heatmaps
+pheatmap(test)
 ```