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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