go.details {gcExplorer} | R Documentation |
Plot or extract size, members or data of a functional group
## S4 method for signature 'data.frame': go.details(object, mvalues, gn, id, stats, links, gonr, source.id, source.group, details = c("size", "names", "id", "data"), table = TRUE, file = "go.details", plot = TRUE, cexl = 0.8, xlab = "", xlabels = NULL, ylab = "M", ylim = c(-6,6), cex.axis = 1, ...)
object |
An object of class "data.frame" . |
mvalues |
Vector giving the columns in object which correspond to the gene expression values. |
gn |
Column of object which corresponds to the gene names used for representation. |
id |
Column of object which corresponds to the unique IDs of the same type as given in source.id . |
links |
Column of object which corresponds to links to database. |
stats |
Column(s) of object which correspond to statistics. |
gonr |
Unique identifier from source.group giving the group of genes to be extracted. |
source.id |
Vector of gene IDs assigned to functional groups given in source.group . |
source.group |
Vector of the same length as source.id . |
details |
The type of details to be extracted. |
table |
Logical. Should an html table be created. |
file |
The file where the output of 'gotable' will be written. |
plot |
Logical. Should the genes be plotted. |
cexl |
Point size of the legend. |
xlab |
Label for the x-axis. |
xlabels |
Either a numeric vector of time points giving the positions on the x-axis or a character vector with names of the positions on the x-axis. |
ylab |
Label for the y-axis. |
ylim |
Range of the y-axis. |
cex.axis |
Point size of the axis. |
... |
Further arguments can be passed to matplot or write.htmltable . |
Theresa Scharl
data(fitsod) data(gobp) ## Plot the functional group go.details(fitsod, mvalues = 2:9, gn = 31, id = 33, links = 35, stats = 26, gonr = "flagellar", source.group = gobp[,3], source.id = gobp[,1], plot = TRUE) ## A file named "go.details.html" will be created in the current ## working directory. go.details(fitsod, mvalues = 2:9, gn = 31, id = 33, links = 35, stats = 26, gonr = "flagellar", source.group = gobp[,3], source.id = gobp[,1], table = TRUE) ## Names of the genes in functional group "flagellar" go.details(fitsod, mvalues = 2:9, gn = 31, id = 33, links = 35, stats = 26, gonr = "flagellar", source.group = gobp[,3], source.id = gobp[,1], details = "names") ## Gene expression values of the functional group d1 <- go.details(fitsod, mvalues = 2:9, gn = 31, id = 33, links = 35, stats = 26, gonr = "flagellar", source.group = gobp[,3], source.id = gobp[,1], details = "data") dim(d1)