cluster_GO {GOexpress} | R Documentation |
Clusters the samples using only the expression levels of genes associated with a given go_id.
cluster_GO( go_id, result, eSet, f=result$factor, subset=NULL, method_dist="euclidean", method_hclust="average", cex=0.8, main=paste(go_id, result$GO[result$GO$go_id == go_id, "name_1006"]), xlab="Distance", cex.main=1, main.Lsplit=NULL, ...)
go_id |
A Gene Ontology (GO) identifier. |
result |
The output of |
eSet |
|
f |
The grouping factor in |
subset |
A named list to subset |
method_dist |
The method used to calculate distance between samples. See the
|
method_hclust |
The method used to cluster samples. See the
|
cex |
A numeric value defining the character expansion of text in the plot. |
main |
A character string for the main title of the plot. |
xlab |
A label for the x axis, defaults to "Distance". |
cex.main |
Scaling factor of the main title font size. Default is 1. We suggest to
use it in combination with the argument |
main.Lsplit |
Number of characters after which a new-line character will be inserted in the main title. If this would occur within a word, the new-line character will be inserted before this word. Default is NULL, leaving the title on a single line. |
... |
Additional parameters passed on to |
Returns the output of the plot()
function.
Kevin Rue-Albrecht
Method GO_analyse
.
# load the sample output data data(AlvMac_results) # Hierarchical clustering of samples based on the same GO term cluster_GO( go_id="GO:0034142", result=AlvMac_results, eSet=AlvMac, cex=0.7 ) # Re-label sample by another factor cluster_GO( go_id="GO:0034142", result=AlvMac_results, eSet=AlvMac, cex=0.7, f="Group" )