Produces a Polar plot, mapping p-values to chromosome location. This
function is used by
1 2 3
character string giving the name of the chromosome
mapping file, or an object of class
character vector of colors to be used by the Polar plot.
should the figures be saved? Defaults to
verbose? Defaults to
This function is mainly used by
diffExp but can also be used
separately by the user.
chromosomeMapping should be either a
or a tab delimited text file and include the columns chromosome with
the chromosome name and chromosome location containing the starting
position of each gene. A
- sign can be used to denote the antisense
strand but this will be disregarded while plotting. The rownames should be
probe IDs or, if using a text file, the first column with a column
header should contain the probe IDs. If relying on an
ArrayData object (called
arrayData) and containing an
annotation field, the
chromosomeMapping can be set to
arrayData$annotation[,c(2,3)] (see the example below).
The Polar plot sorts the genes according to chromosomal location, for each chromosome starting with unknown positions followed by increasing number in the chromosome location column. Genes which do not map to any chromosome are listed as U for unknown. The radial lines in the Polar plot are -log10 scaled p-values, so that a longer line means a smaller p-value. This gives an overview of the magnitude of differential expression for each contrast.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17
# Get path to example data and setup files: dataPath <- system.file("extdata", package="piano") # Load normalized data: myArrayData <- loadMAdata(datadir=dataPath, dataNorm="norm_data.txt.gz", platform="yeast2") # Perform differential expression analysis: pfc <- diffExp(myArrayData, plot=FALSE, contrasts=c("aerobic_Clim - anaerobic_Clim", "aerobic_Nlim - anaerobic_Nlim")) # Get chromosome mapping from myArrayData: chrMap <- myArrayData$annotation[,c(2,3)] # Get p-values from pfc pval <- pfc$pValues # Draw the polar plot: polarPlot(pval, chromosomeMapping=chrMap)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.