Heatmap in R studio

Heatmap is a graphical representation for data with different magnitude that is illustrated by colors. Here, we have used a cervical cancer data for visualization of heatmap.

cervical_cancer

.xlsx

Download XLSX • 247KB

install.packages("gplots")    #uploads heatmap function
library("gplots")    
dim(cervical_cancer)          #dimension(dim) tells us the number of 
                              rows and columns  (117 143 in this case)
                       
c_cancer <- as.matrix(cervical_cancer[, c(2:143)]) 
*For heatmap we want data in form of matrix to represent the values
therefore we create c_cancer using function as.matrix selecting from 2nd column to 143    

 heatmap.2 (c_cancer,
 scale = "row",              #used for normalization of data in rows 
 trace = "none",             #removes trace lines from heatmap 
 Colv  =  NA)                #removes dendrogram from columns 
 

Changing Color Palette

library("RColorBrewer")

color_palette <- colorRampPalette(brewer.pal(8, "YlGn")
#here 8 is the number of colors with Yellow and Green (YlGn) colors

library("gplots")
dim(cervical_cancer)
c_cancer <- as.matrix(cervical_cancer [, c(2:143)])
heatmap.2(c_cancer,
scale = "row",
trace = "none",
col   =  color_palette,   #changing color palette
main  =  "Heatmap")