Usage
genespca(x, ntop, choices = c(1, 2), arrowColors = "steelblue",
groupNames = "group", biplot = TRUE, scale = 1, pc.biplot = TRUE,
obs.scale = 1 - scale, var.scale = scale, groups = NULL,
ellipse = FALSE, ellipse.prob = 0.68, labels = NULL, labels.size = 3,
alpha = 1, var.axes = TRUE, circle = FALSE, circle.prob = 0.69,
varname.size = 4, varname.adjust = 1.5, varname.abbrev = FALSE,
returnData = FALSE, coordEqual = FALSE, scaleArrow = 1,
useRownamesAsLabels = TRUE, point_size = 2, annotation = NULL)
Arguments
ntop
Number of top genes to use for principal components,
selected by highest row variance
choices
Vector of two numeric values, to select on which principal components to plot
arrowColors
Vector of character, either as long as the number of the samples, or one single value
groupNames
Factor containing the groupings for the input data. Is efficiently chosen
as the (interaction of more) factors in the colData for the object provided
biplot
Logical, whether to additionally draw the samples labels as in a biplot representation
scale
Covariance biplot (scale = 1), form biplot (scale = 0). When scale = 1,
the inner product between the variables approximates the covariance and the
distance between the points approximates the Mahalanobis distance.
pc.biplot
Logical, for compatibility with biplot.princomp()
obs.scale
Scale factor to apply to observations
var.scale
Scale factor to apply to variables
groups
Optional factor variable indicating the groups that the observations
belong to. If provided the points will be colored according to groups
ellipse
Logical, draw a normal data ellipse for each group
ellipse.prob
Size of the ellipse in Normal probability
labels
optional Vector of labels for the observations
labels.size
Size of the text used for the labels
alpha
Alpha transparency value for the points (0 = transparent, 1 = opaque)
var.axes
Logical, draw arrows for the variables?
circle
Logical, draw a correlation circle? (only applies when prcomp
was called with scale = TRUE and when var.scale = 1)
circle.prob
Size of the correlation circle in Normal probability
varname.size
Size of the text for variable names
varname.adjust
Adjustment factor the placement of the variable names,
>= 1 means farther from the arrow
varname.abbrev
Logical, whether or not to abbreviate the variable names
returnData
Logical, if TRUE returns a data.frame for further use, containing the
selected principal components for custom plotting
coordEqual
Logical, default FALSE, for allowing brushing. If TRUE, plot using
equal scale cartesian coordinates
scaleArrow
Multiplicative factor, usually >=1, only for visualization purposes,
to allow for distinguishing where the variables are plotted
useRownamesAsLabels
Logical, if TRUE uses the row names as labels for plotting
point_size
Size of the points to be plotted for the observations (genes)
annotation
A data.frame object, with row.names as gene identifiers (e.g. ENSEMBL ids)
and a column, gene_name, containing e.g. HGNC-based gene symbols