read.table() # read a text-format matrix into R as.matrix() # coerce a data structure into matrix form c() # create a column vector containing listed elements dim() # Return the dimensionality of the indicated structure

[] #Use square brackets to indicate subset of data structure #e.g. tmp[2:5,12:20] returns rows 2-5 of columns 12:20

{} #Use curly braces to group several different commands together before #executing them.

for (i1 in c (1:10)) #Use the for statment to iterate through a column vector #On each loop i1 will take on the next value in the #specified vector, then the command following the for #loop will be executed once.

barplot(c(), beside = T) #Plot a column vector as a parplot. #Use ylim = c(min,max) to set min and max values for the #y axis.

dist(matrix) #Returns the Euclidean distances between #all rows of the matrix indicated. To inspect/visualize this #it should be converted to a matrix using as.matrix()

image(dmatrix) #Plots a heat map of the supplied matrix. This is useful #for visualizing distance matrices. By default the matrix is #is plotted "backwards"; to see it in the canonical orientation #you need to reverse-index the columns: image(dmatrix[,n:1]), #where n=total number of columns

hclust(distance) #compute a hierarchical clustering based on the items in #the supplied distance matrix.

cmdscale(distance) #compute a multidimensional scaling of the distance matrix

plot() #Generic plotting function. If applied to a 2-column matrix, generates #a scatterplot. If applied to the results of hclust, generates a #hierarchical cluster plot.

lines() #Add lines to the existing plots. points() #Add points to the existing plots text() #Add text to the existing plots

Some useful arguments for plotting functions:

type = "l" #Connects successive points with a line type = "o" #Plots both points and lines type = "n" #Sets up the axes but doesn't actually plot any data

xlab, ylab = "Axis labels" #Sets name for xaxis xlim, ylim = c(x,y) # sets the minimum (x) and maximum (y) value # for the x / y axes lwd = x #Sets line width lty = x #Sets line type (1 = solid, 2 = dashed, etc) lcol = x #Sets line color

pch = x #Sets shape to use as point marker (use integer)

mtext(text, line, at, las) Plots test in the margines. text is a vector #containing words to be plotted; line indicates #how far from the edge it should be; at indicates #where along the figure the text should appear; #las indicates the orientation of the text.