image {maigesPack} | R Documentation |
Generic function image
to display colour maps
of numerical values stored in objects defined in this package.
## S3 method for class 'maigesRaw': image(x, ...) ## S3 method for class 'maiges': image(x, ...) ## S3 method for class 'maigesANOVA': image(x, ...) ## S3 method for class 'maigesRelNetB': image(x=NULL, name=NULL, ...) ## S3 method for class 'maigesRelNetM': image(x=NULL, names=NULL, ...) ## S3 method for class 'maigesActMod': image(x, type=c("S","C")[2], keepEmpty=FALSE, ...) ## S3 method for class 'maigesActNet': image(x, type=c("score","p-value")[1], ...)
x |
an object of class maigesRaw ,
maiges , maigesANOVA ,
maigesRelNetB , maigesRelNetM ,
maigesActMod or maigesActNet defined in
this package. |
name |
character string giving a name for sample type tested to
be plotted as a name in the method for class maigesRelNetB . |
names |
similar to the previous one, but it is a vector of length
3 for class maigesRelNetM . |
type |
string specifying the type of colour map to be plotted. For
class maigesActMod it must be 'S' or 'C' for samples
or biological conditions, respectively. For class
maigesActNet it must be 'score' or 'p-value' for the
statistics or p-values of the tests, respectively. |
keepEmpty |
logical, if true the results of all gene groups are displayed, else only the gene groups that present at least one significant result are displayed. |
... |
additional arguments for the generic method
image from graphics package or
maImage defined in package marray (for
maigesRaw , maiges or maigesANOVA classes), in
this case the additional parameters must not be named, because these
names conflict with the boxplot generic function definition. |
This method uses the function maImage
from
marray package to display colour maps of accessor methods defined into
marray package for objects of class maiges
or
maigesRaw
and maigesANOVA
.
For objects of class
maigesRelNetM
the method displays 3 colour maps
representing the correlation values for the two groups tested and the
p-values of the tests.
For class maigesRelNetB
it
displays the correlation values for the type tested.
In objects of
class maigesActMod
it displays the fraction of genes
induced or repressed for each gene group, by samples or biological
type.
Finally, for class maigesActNet
, the method
display the matrix of statistics or p-values of the tests.
Pay attention, if you specify the parameter x (but not named)
for maImage
) it will plot the M values instead
of W (default).
Gustavo H. Esteves <gesteves@vision.ime.usp.br>
image
in the graphics package and
maImage
in marray package.
## Loading the dataset data(gastro) ## Doing image plots (using package marray), default method showing the ## W values (for 1st chip), after showing the A values (2nd chip) and ## red background (20th chip). image(gastro.raw[,1]) image(gastro.raw[,2], "maA") image(gastro.raw[,20], "maRb") ## Example for normalized objects (showing A values for the 5th chip). image(gastro.norm[,5], "maA") ## Example for object of class maigesRelNetB ## Constructing the relevance network (Butte's method) for sample ## 'Tissue' equal to 'Neso' for the 1st gene group gastro.net = relNetworkB(gastro.summ, sLabelID="Tissue", samples="Neso", geneGrp=1, type="Rpearson") image(gastro.net) ## Example for object of class maigesRelNetM ## Constructing the relevance network for sample ## 'Tissue' comparing 'Neso' and 'Aeso' for the 1st gene group gastro.net = relNetworkM(gastro.summ, sLabelID="Tissue", samples = list(Neso="Neso", Aeso="Aeso"), geneGrp=11, type="Rpearson") image(gastro.net)