R function - heatmap.2

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library(gplots)
library(RColorBrewer)

# Use the data frame "mtcars" as an example, and transform to a matrix
data(mtcars)
cars <- as.matrix(mtcars) # A matrix with row and column names; 
                          # you can set names with the functions 
                          # "rownames" and "colnames" for other data sets.

# Some pre-defined parameters will be used afterward
cols <- colorRampPalette(c("gray",
    "yellow","red"))(100) # interpolate the given three colors 
                          # to create new color palettes with 100 colors.

colCols <- ifelse(colnames(cars)>"m","purple",
    ifelse(colnames(cars)>"f","lightblue","red")) # set colors for the column names arbitrary.

rowCols <- ifelse(rownames(cars)>"m","purple",
    ifelse(rownames(cars)>"f","lightblue","red")) # set colors for the row names arbitrary.

# The main function, and comments for frequently-used arguments. 
# See Fig. 1 for the representation.
heatmap.2(
    cars, # a numeric matrix

    Rowv=TRUE, # if and how the row dendrogram should be reordered, 
               # default value is TRUE.

    Colv=TRUE, # if and how the column dendrogram should be reordered, 
               # always equal to "Rowv".

    distfun=function(x) 
      {dist(x,method="manhattan")}, # function used to compute the distance between 
                                    # both rows and columns. The default is Euclidean distance, 
                                    # but you can change it (Notice, there is a function).

    hclustfun=function(x) 
      {hclust(x,method="average")}, # function used to compute the hierarchical 
                                    # clustering when "Rowv" or "Colv" are not dendrograms. 

    dendrogram="both", # draw dendrogram(s) for "row", "column", or "both", or "none".

    scale="column", # should normalize the values in "row" direction 
                    # or the "column" direction, or neither ("none").

    na.rm=TRUE, # whether the NAs should be removed.
    
    col=cols, # colors for the image, many many options, 
              # search for the functions "colorRampPalette", 
              # "rainbow", "colorpanel", "brewer.pal" ... 
              # then improve your figures.
    
    cellnote=ifelse(abs(scale(cars))>2,'Y','N') , # a matrix of character strings 
                                                  # which will be placed in each cell. 
                                                  # I check whether the absolute scaled values 
                                                  # bigger than 2 (not very useful here).

    notecex=0.8, # the size of "cellnote" (a scaling factor).

    notecol="black", # color for "cellnote".
    
    trace="column", # should a solid trace be drawn across "column", 
                    # "row", "both" or "none".

    tracecol="white", # color for the trace

    margin=c(5,10), # margins for column and row names, respectively.

    ColSideColors=colCols, # a vector of colors for the horizontal 
                           # side bar used to annotate the columns. 

    RowSideColors=rowCols, # a vector of colors for the vertical 
                           # side bar used to annotate the rows.

    key=TRUE, # whether a color key should be shown.

    keysize=1.2, # the size of the color key.

    density.info="density", # whether to superimpose a "histogram", 
                            # "density" or "none" on the color key.

    denscol="black", # the color for the "density".

    key.title="Color key", # main title of the color key. "NA" for no title.

    key.xlab=NULL, # x label of the color key. 
                   # "NULL" for automatic label which is 
                   # related to the "density.info" you used.

    key.ylab=NULL, # y label of the color key.

    main="Heat map example", # main title.

    xlab="Column names", # x axis title.

    ylab="Row names" # y axis title.
    
)