geneImager {compdiagTools} | R Documentation |
This function creates a 'compdiag style' blue-yellow cluster
plot. With no given filename the image is plotted to x11().
If a filename is given the image is plotted into a file and a
corresponding HTML image map is returned. The links provided
in the map are generated either from annotProbes
elements
themselves, or (if they exist) from their associated element names
names(annotProbes)
.
geneImager(data, chip, cluster="both", dendro="both", center = TRUE, scale=FALSE, outputPath=".", file=NULL, zlim=NULL, annotSamples=NULL, annotProbes=NULL, forceExceed=FALSE, x_max=NULL, y_max=NULL, hide.colorbar = FALSE, sample.group = NULL, group.bgc = NULL, group.fgc = NULL, heightScale = 1, ...)
data |
numeric matrix of the values to be plotted |
chip |
the chip name as character string to look up gene symbols. |
cluster |
Determines if the data should be clustered. Possible options are: FALSE, "both", "probes" (rows), "samples" (columns) |
dendro |
Determines if dendrograms should be plotted. Possible options are: FALSE, "both", "probes" (rows), "samples" (columns) |
center |
Boolean - indicates if row-wise centering (mean subtract) should be performed. |
scale |
Boolean - indicates if a row-wise scaling should be performed. |
file |
determines the output filename (if no filename is given
the output is plotted to x11()). This is relative to outputPath .
The generated HTML uses only this part of the full filename. |
outputPath |
optional output path for the file.If file is other than
NULL, its concatenation with outputPath is where the image is written. |
zlim |
c(lower,upper) limits on logarithmic scale for colorbar. If not given the limits are calculated from the data as the 2.5% quantile and 97.5% quantile. Data is always truncated according to zlim. |
annotSamples |
Vector of character strings for sample annotation. The x. element in annotSamples has to correspond to the x. column of data. |
annotProbes |
Vector of character strings for probe annotation. The x. element in annotProbes has to correspond to the x. row of data. If this vector is a named vector, associated element names are used as link in the image map. If the vector is not named, the elements themselves are used as link. This can also be NULL, in which case labels are guessed from rownames, or FALSE, where annotations are omitted. |
forceExceed |
Boolean - indicates if internal ploting limits should be exceeded. All given annotations are plotted. Works only in connection with file output |
x_max |
numerical value - maximal size of the x component of the heatmap region (in centimeters), if NULL internal limits are used |
y_max |
numerical value - maximal size of the y component of the heatmap region (in centimeters), if NULL internal limits are used |
hide.colorbar |
avoid showing the color bar on the right hand side. |
sample.group |
one group label per sample is expected. This vector is used to sort samples such that samples with same group labels are grouped together. Clustering overwrites this option. The factor values are displayed on top of the image. |
group.bgc |
background colors used for background of group
annotations. Colors coded as character strings must be provided.
The vector is recycled, if there are more groups than color codes.
The default (NULL) causes geneImager to use alternating
shades of grey. |
group.fgc |
similar to group.bgc for the foreground (text) colors. |
heightScale |
scale the height of the figure (not the data). |
... |
further arguments passed on to bitmap |
If a filename is given: String representing an HTML image map, including <img> tag. If no filename is given: output is printed to x11()
library(hgu95av2) probes <- ls(hgu95av2GENENAME)[1:30] symbols <- unlist(mget(probes,hgu95av2SYMBOL)) probeAnnot <- symbols names(probeAnnot) <- probes expr.data <- cbind(matrix(rnorm(450,3),30,15),matrix(rnorm(450,0),30,15)) expr.data[,1:30] <- expr.data[,sample(1:30)] geneImager(expr.data, annotProbes=probeAnnot, scale=TRUE, cluster="samples", dendro="samples", file="outfile.png") # using geneImager together with geneLister imageMap <- geneImager(expr.data,annotProbes=probeAnnot,scale=TRUE,cluster="samples",dendro="samples",file="example.png") htmlTable <- geneLister(probes,chip="hgu95av2",annotGO=FALSE) write(c(imageMap,htmlTable),file="example.html")