plot-methods: Methods for function 'plot'

In mengchen18/mogsa: Multiple omics data integrative clustering and gene set analysis

Description

Methods for function plot

Methods

list("signature(x = \"moa\", y = \"missing\")")

plot "moa" object

Argument "value" sould be one of "eig", "tau", "obs", "var" and "RV"\

if value = "eig", the eigenvalue would be plotted as scree plot. The following arguments could be set:\

type=1 - The type of plot to show eigenvalues. (type=1: the eigenvalue are plotted; type=2: partial eigenvalue shown as concatenated bars; type=3: partial eigenvalue shown as bars side by side; type=4: matplot view of eigenvales, lty need to be set; type=5; the two dimensional plot of partial eigenvalues, axes and pch need to be set in this case.) \ axes=NULL - The axes selected to plot \ n=NULL - Top n eigenvalues to be drawn \ tol=1e-5 - The tolerance of eigenvalue, eigenvalues lower than this value will not be shown. \ legend=NULL - legend to put, a character string as calling legend function \ col=NULL - The color of partial eigenvalues from each data set \ lty=1 - The line type used in the matplot, used when type =4 \ pch=NULL - the pch to draw 2D partial eigen plot, when type = 5 used \ lg.x="topright" - The position of legend \ lg.y=NULL - Poistion argument passed to function "legend" \ ... - other arguemnts passed to functions \ \

if value = "tau", the same with eig, but in the eigenvalues are scaled to 1 \

if value = "obs", the observation space will be shown, the following argument could be set:\

axes=1:2 - Which axes should be draw\ type=1 - Which type, see below (for type=1: the center points draw; type=2: the separate factor scores linked by lines; ... will be passed to function "points")\ data.pch=20 - the pch of dataset, if type=1, the first one is used\ col=1 - the color of observations, recycled used by data.frame\ label=FALSE - A logical indicates if labels should be shown\ lg.x="topright" - Position of legend \ lg.y=NULL - Position of legend \ xlim=NULL - The x limit \ ylim=NULL - The y limit \ label.cex=1 - the cex of text \ ... \

var - the separate gene view, layout can be specified \

RV - the heatmap of RV coefficients

mengchen18/mogsa documentation built on June 7, 2020, 6:05 p.m.