plotLong | R Documentation |
This function provides a expression profile representation over time and by cluster.
plotLong(
object,
time = NULL,
plot = TRUE,
center = TRUE,
scale = TRUE,
title = "Time-course Expression",
X.label = NULL,
Y.label = NULL,
legend = FALSE,
legend.title = NULL,
legend.block.name = NULL
)
object |
a mixOmics result of class (s)pca, (s)pls, block.(s)pls. |
time |
(optional) a numeric vector, the same size as |
plot |
a logical, if TRUE then a plot is produced. Otherwise, the data.frame on which the plot is based on is returned. |
center |
a logical value indicating whether the variables should be shifted to be zero centered. |
scale |
a logical value indicating whether the variables should be scaled to have unit variance before the analysis takes place. |
title |
character indicating the title plot. |
X.label |
x axis titles. |
Y.label |
y axis titles. |
legend |
a logical, to display or not the legend. |
legend.title |
if |
legend.block.name |
a character vector corresponding to the size of the number of blocks in the mixOmics object. |
a data.frame (gathered form) containing the following columns:
time |
x axis values |
molecule |
names of features |
value |
y axis values |
cluster |
assigned clusters |
block |
name of 'blocks' |
getCluster
demo <- suppressWarnings(get_demo_cluster())
X <- demo$X
Y <- demo$Y
Z <- demo$Z
# (s)pca
pca.res <- mixOmics::pca(X, ncomp = 3)
plotLong(pca.res)
spca.res <- mixOmics::spca(X, ncomp =2, keepX = c(15, 10))
plotLong(spca.res)
# (s)pls
pls.res <- mixOmics::pls(X,Y)
plotLong(pls.res)
spls.res <- mixOmics::spls(X,Y, keepX = c(15,10), keepY=c(5,6))
plotLong(spls.res)
# (s)block.spls
block.pls.res <- mixOmics::block.pls(X=list(X=X,Z=Z), Y=Y)
plotLong(block.pls.res)
block.spls.res <- mixOmics::block.spls(X=list(X=X,Z=Z), Y=Y,
keepX = list(X = c(15,10), Z = c(5,6)),
keepY = c(3,6))
plotLong(block.spls.res)
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