CODEWITHSUNDEEP
rheatmap
mchapak
mchapak

Reputation: 1

Generating heat maps in R with ordered columns & rows

I would like to generate a heat map using an ordered 6x6 matrix. This is the code I have used:

mat_data <- data.matrix(data[,2:ncol(data)])  # transform column 2-7 into a matrix
rownames (data) <- c("1","2","3","4", "5", "6")
colnames (data) <- c("1","2","3","4", "5", "6")

png("..../trial.png",    # create PNG for the heat map        
width = 5*300,        # 5 x 300 pixels
height = 5*300,
res = 300,            # 300 pixels per inch
pointsize = 8)        # smaller font size

heatmap.2(mat_data, 
    cellnote = mat_data,  # same data set for cell labels
    main = "Trial",       # heat map title
    notecol="black",      # change font color of cell labels to black
    density.info="none",  # turns off density plot inside color legend
    trace="none",         # turns off trace lines inside the heat map
    margins =c(8,9),      # widens margins around plot
    col=my_palette,       # use on color palette defined earlier 
    dendrogram="none",    # no dendrogram
    Rowv = "FALSE",
    Colv="FALSE")         # turn off column clustering

dev.off()                 # close the PNG device

I want the rows ordered 1-6 across, and columns ordered 6-1 from top to bottom starting at the lower left hand box, such that the map is paired 1-1 at (row, column) (6,1), 2-1 at (6,2), 3-1 at (6,3)...etc

Kindly assist on how to change the order, thanks.

Upvotes: 0

Views: 1228

Answers (1)

Miff
Miff

Reputation: 7951

library(gplots)

#Create sample data
mat_data <- matrix(runif(36),6)  # transform column 2-7 into a matrix
rownames (mat_data) <- c("1","2","3","4", "5", "6")            ##mat_data, data doesn't exist
colnames (mat_data) <- c("1","2","3","4", "5", "6")

png("..../trial.png",    # create PNG for the heat map
width = 5*300,        # 5 x 300 pixels
height = 5*300,
res = 300,            # 300 pixels per inch
pointsize = 8)        # smaller font size



heatmap.2(mat_data[6:1,],  #Change row order
    cellnote = mat_data,  # same data set for cell labels
    main = "Trial",       # heat map title
    notecol="black",      # change font color of cell labels to black
    density.info="none",  # turns off density plot inside color legend
    trace="none",         # turns off trace lines inside the heat map
    margins =c(8,9),      # widens margins around plot
#    col=my_palette,       # use on color palette defined earlier - doesn't exist
    dendrogram="none",    # no dendrogram
    Rowv = "FALSE",
    Colv="FALSE")         # turn off column clustering

dev.off()                 # close the PNG device

Upvotes: 1

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