glMDSPlot.DGEList {Glimma} | R Documentation |
Draw an interactive MD plot from a DGEList object with distances calculated from most variable genes.
## S3 method for class 'DGEList' glMDSPlot( x, top = 500, labels = NULL, groups = rep(1, ncol(x)), gene.selection = c("pairwise", "common"), prior.count = 2, main = "MDS Plot", path = getwd(), folder = "glimma-plots", html = "MDS-Plot", launch = TRUE, ... )
x |
the DGEList containing the gene expressions. |
top |
the number of top most variable genes to use. |
labels |
the labels for each sample. |
groups |
the experimental group to which samples belong. |
gene.selection |
"pairwise" if most variable genes are to be chosen for each pair of samples or "common" to select the same genes for all comparisons. |
prior.count |
average count to be added to each observation to avoid taking log of zero. Used only if log=TRUE. |
main |
the title of the plot. |
path |
the path in which the folder will be created. |
folder |
the name of the fold to save html file to. |
html |
the name of the html file to save plots to. |
launch |
TRUE to launch plot after call. |
... |
additional arguments. |
Draws a two-panel interactive MDS plot in an html page. The left panel contains the plot between two MDS dimensions, with annotations displayed on hover. The right panel contains a bar plot of the eigenvalues of each dimension, clicking on any of the bars will plot the corresponding dimension against the next dimension.
Shian Su, Gordon Smyth