arrayview {maanova} | R Documentation |
This function reconstructs the input data according to the micro array grid location structure and plots the data according to the user specified color map.
Dy default, it will plot the log ratios for 2-dye array and raw intensity for 1-dye array. It doesnot work for N-dye (N>2) array at this time.
Note that if user collapsed the replicates in creating the
madata
object (see createData
),
arrayview will be unavailable.
arrayview(object, ratio, array, colormap, onScreen=TRUE, ...)
object |
An object of class madata or rawdata . |
ratio |
The data to be ploted. The length of it must be
equal to the length of the grid locations, .e.g, madata$row and
madata$col. If ratio is a vector, there will be one plot. If ratio
is a matrix, there will be one plot for each column. If ratio is not
provided, link[maanova]{make.ratio} will be called to
calculate the ratios from the original data. |
array |
A list of arrays to be plotted. This variable is only
valid when ratio is not provided. Whenever ratio is
provided, all columns in ratio will be plotted. |
colormap |
User specified color map. See
colors for more detail. |
... |
Other parameters to be passed to
image . |
onScreen |
A logical value to represent whether to display the plots on screen or not. If TRUE, x11() (in Unix/Windows) or macintosh (in Mac) will be called inside the function. Otherwise, it will plot the figure on the current device. Default is TRUE. |
Hao Wu
## Not run: data(kidney) ############################ # arrayview plot on rawdata ############################ # arrayview raw data on screen arrayview(kidney.raw, array=1) graphics.off() # arrayview raw data array 1 and 3 and output to postscript file postscript(file="kidneyArrayview.ps") arrayview(kidney.raw, array=c(1,3), onScreen=FALSE) ## End(Not run) # once the replicates are collapsed, # arrayview will be unavailable ## Not run: data1 <- createData(kidney.raw, n.rep=2, avgreps=1) ## Not run: arrayview(data1) # get an error here