spectralMap {a4Base} | R Documentation |
Generic function to draw a spectral map, according to JnJ Standards
spectralMap(object, groups, ...)
object |
object of class ExpressionSet |
groups |
string indicating the name of the column in the phenoData that defines the groups |
... |
further arguments to be passed to the methods |
Object of class plot.mpm
, i.e. the S3 output object of the plot.mpm
function of the mpm
package
Coloring of groups on the spectralMap uses the a4 palette as produced
by a4palette
Tobias Verbeke
Wouters, L., Goehlmann, H., Bijnens, L., Kass, S.U., Molenberghs, G., Lewi, P.J. (2003). Graphical exploration of gene expression data: a comparative study of three multivariate methods. Biometrics 59, 1131-1140. Goehlmann, H. and W. Talloen (2009). Gene Expression Studies Using Affymetrix Microarrays, Chapman \& Hall/CRC, pp. 148 - 153.
if (require(ALL)){ data(ALL, package = "ALL") ALL <- addGeneInfo(ALL) spectralMap(object = ALL, groups = "BT", legendPos = 'bottomright') spectralMap(object = ALL, groups = "BT", plot.mpm.args = list(label.tol = 10, rot = c(-1, 1), sub = "", lab.size = 0.65, dim = c(1,2), sampleNames = FALSE, zoom = c(1,5), col.size = 2, do.smoothScatter = TRUE)) spectralMap(object = ALL, groups = "BT", plot.mpm.args = list(label.tol = 10, rot = c(-1, 1), sub = "", lab.size = 0.65, dim = c(1,2), sampleNames = as.character(pData(ALL)$BT), zoom = c(1,5), col.size = 2, do.smoothScatter = TRUE)) }