ggbootMV: mv med plot info func

Description Usage Arguments Details

View source: R/ggbootMV.R

Description

x PCA biplot with bootstrap confidence areas.

Usage

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ggbootMV(data, group, B, seed = NULL, comp = 1:2, locType = "mean",
  scale = FALSE, checkPlot = FALSE, dispPlot = FALSE, labelVec = NULL,
  legendTitle = "Group", colVec = c("darkorchid1", "springgreen2",
  "maroon1", "dodgerblue", "red", "yellow3", "cyan2", "orange2"),
  addOrigPos = TRUE, pcaAxesLabSize = 2.5, origPosLabSize = 2,
  axes = TRUE, points = TRUE, pointAlpha = 1, pointSize = 1,
  ellipse = TRUE, ellAlpha = 1, ellSize = 1, quant = FALSE,
  quantAlpha = 1, quantSize = 1, density = FALSE, densAlpha = 1,
  densSize = 1, boot = TRUE, save = FALSE, name = NULL, env = NULL,
  path = NULL, textAdjVal = 0.2, axesLenRatio = NULL, qualCutoff = 0,
  selAxisLab = NULL, arrow = FALSE, arrowSize = 2, fontScaleFactor = 1)

Arguments

data

dataframe. In wide format. Only numeric columns will be used.

group

vector. Vector indicating group membership for each observation in data. Will be coerced to a character vector.

B

integer. Number of bootstrap samples per subgroup.

comp

integer vector. Specifies the principal components whose proportion of variation must be returned. Defaults to 1:2.

locType

character. Specifies measure of location to use. Options are mean, cmwed (column-wise median), oja, weisz (geometric median) and gmed (a fast version for the geometric median).

pointSize

numeric. Size of plot points

quant

logical. If TRUE, then univariate 95 percent percentile bootstrap confidence intervals are plotted.

boot

logical. If TRUE, then bootstrap is re-performed. If FALSE, then bootstrap values are taken from object with name name in environment bootList.

save

logical. If TRUE and boot=TRUE, then bootList is

name

character. Name of object in bootList to add to or take to. Must not be NULL if save=TRUE.

env

environment. Environment to save bootstrapped values to.

path

character. Path of to save bootstrapped values to, or load bootstrapped values from.

textAdjVal

numeric. Value that controls the degree to which the axis labels are shifted from the endpoints of the axes. Higher values move the axis further right and up.

axesLenRatio

numeric. If not NULL, then the ratio of the length of the y-axis divided by the x-axis is made equal to axesLenRatio, where length is defined as the difference between the maximum and the minimum value plotted along that axis. This is done by stretching the shorter axis around its mean. Useful for making the axes of equal length.

qualCutoff

numberic. The minimum sum of the axis predictivity across the principal components selected (by comp) required for the axis of a variable to be plotted. Only works if arrow=FALSE (this will change in future).

selAxisLab

character vector. Names of columns in data to print.

arrow

logical. If TRUE, then arrows instead of lines are plotted for the axes. The arrows point from the origin to the largest observed value for its variable on the biplot axis.

arrowSize

numeric. Size of the arrows for ggplot2 to use.

fontScaleFactor

numeric. Ratio by which to multiply the default font size.

Details

Plot a PCA biplot with bootstrap confidence ares.


MiguelRodo/ggboot documentation built on May 1, 2018, 12:22 a.m.