biplot {PCAtools} | R Documentation |
Draw a bi-plot, comparing 2 selected principal components / eigenvectors.
biplot( pcaobj, x = "PC1", y = "PC2", showLoadings = FALSE, ntopLoadings = 5, showLoadingsNames = if (showLoadings) TRUE else FALSE, colLoadingsNames = "black", sizeLoadingsNames = 3, boxedLoadingsNames = TRUE, fillBoxedLoadings = alpha("white", 1/4), drawConnectorsLoadings = TRUE, widthConnectorsLoadings = 0.5, colConnectorsLoadings = "grey50", lengthLoadingsArrowsFactor = 1.5, colLoadingsArrows = "black", widthLoadingsArrows = 0.5, alphaLoadingsArrow = 1, colby = NULL, colkey = NULL, colLegendTitle = if (!is.null(colby)) colby else NULL, singlecol = NULL, shape = NULL, shapekey = NULL, shapeLegendTitle = if (!is.null(shape)) shape else NULL, pointSize = 3, legendPosition = "none", legendLabSize = 12, legendTitleSize = 14, legendIconSize = 5, encircle = FALSE, encircleFill = TRUE, encircleFillKey = NULL, encircleAlpha = 1/4, encircleLineSize = 0.25, encircleLineCol = NULL, ellipse = FALSE, ellipseType = "t", ellipseLevel = 0.95, ellipseSegments = 51, ellipseFill = TRUE, ellipseFillKey = NULL, ellipseAlpha = 1/4, ellipseLineSize = 0.25, ellipseLineCol = NULL, xlim = if (showLoadings || ellipse) c(min(pcaobj$rotated[, x]) - abs((min(pcaobj$rotated[, x])/100) * 35), max(pcaobj$rotated[, x]) + abs((min(pcaobj$rotated[, x])/100) * 35)) else c(min(pcaobj$rotated[, x]) - abs((min(pcaobj$rotated[, x])/100) * 10), max(pcaobj$rotated[, x]) + abs((min(pcaobj$rotated[, x])/100) * 10)), ylim = if (showLoadings || ellipse) c(min(pcaobj$rotated[, y]) - abs((min(pcaobj$rotated[, y])/100) * 35), max(pcaobj$rotated[, y]) + abs((min(pcaobj$rotated[, y])/100) * 35)) else c(min(pcaobj$rotated[, y]) - abs((min(pcaobj$rotated[, y])/100) * 10), max(pcaobj$rotated[, y]) + abs((min(pcaobj$rotated[, y])/100) * 10)), lab = rownames(pcaobj$metadata), labSize = 3, boxedLabels = FALSE, selectLab = NULL, drawConnectors = TRUE, widthConnectors = 0.5, colConnectors = "grey50", max.overlaps = 15, maxoverlapsConnectors = NULL, min.segment.length = 0, directionConnectors = "both", xlab = paste0(x, ", ", round(pcaobj$variance[x], digits = 2), "% variation"), xlabAngle = 0, xlabhjust = 0.5, xlabvjust = 0.5, ylab = paste0(y, ", ", round(pcaobj$variance[y], digits = 2), "% variation"), ylabAngle = 0, ylabhjust = 0.5, ylabvjust = 0.5, axisLabSize = 16, title = "", subtitle = "", caption = "", titleLabSize = 16, subtitleLabSize = 12, captionLabSize = 12, hline = NULL, hlineType = "longdash", hlineCol = "black", hlineWidth = 0.4, vline = NULL, vlineType = "longdash", vlineCol = "black", vlineWidth = 0.4, gridlines.major = TRUE, gridlines.minor = TRUE, borderWidth = 0.8, borderColour = "black", returnPlot = TRUE )
pcaobj |
Object of class 'pca' created by pca(). |
x |
A principal component to plot on x-axis. All principal component names are stored in pcaobj$label. |
y |
A principal component to plot on y-axis. All principal component names are stored in pcaobj$label. |
showLoadings |
Logical, indicating whether or not to overlay variable loadings. |
ntopLoadings |
If showLoadings == TRUE, select this many variables based on absolute ordered variable loading for each PC in the biplot. As a result of looking across 2 PCs, it can occur whereby greater than this number are actually displayed. |
showLoadingsNames |
Logical, indicating to show variable loadings names or not. |
colLoadingsNames |
If 'showLoadings == TRUE', colour of text labels. |
sizeLoadingsNames |
If 'showLoadings == TRUE', size of text labels. |
boxedLoadingsNames |
Logical, if 'showLoadings == TRUE', draw text labels in boxes. |
fillBoxedLoadings |
When 'boxedLoadingsNames == TRUE', this controls the background fill of the boxes. To control both the fill and transparency, user can specify a value of the form 'alpha(<colour>, <alpha>)'. |
drawConnectorsLoadings |
If 'showLoadings == TRUE', draw line connectors to the variable loadings arrows in order to fit more labels in the plot space. |
widthConnectorsLoadings |
If 'showLoadings == TRUE', width of the line connectors drawn to the variable loadings arrows. |
colConnectorsLoadings |
If 'showLoadings == TRUE', colour of the line connectors drawn to the variable loadings arrows. |
lengthLoadingsArrowsFactor |
If 'showLoadings == TRUE', multiply the internally-determined length of the variable loadings arrows by this factor. |
colLoadingsArrows |
If showLoadings == TRUE, colour of the variable loadings arrows. |
widthLoadingsArrows |
If showLoadings == TRUE, width of the variable loadings arrows. |
alphaLoadingsArrow |
If showLoadings == TRUE, colour transparency of the variable loadings arrows. |
colby |
If NULL, all points will be coloured differently. If not NULL, value is assumed to be a column name in pcaobj$metadata relating to some grouping/categorical variable. |
colkey |
Vector of name-value pairs relating to value passed to 'col', e.g., c(A='forestgreen', B='gold'). |
colLegendTitle |
Title of the legend for the variable specified by 'colby'. |
singlecol |
If specified, all points will be shaded by this colour. Overrides 'col'. |
shape |
If NULL, all points will be have the same shape. If not NULL, value is assumed to be a column name in pcaobj$metadata relating to some grouping/categorical variable. |
shapekey |
Vector of name-value pairs relating to value passed to 'shape', e.g., c(A=10, B=21). |
shapeLegendTitle |
Title of the legend for the variable specified by 'shape'. |
pointSize |
Size of plotted points. |
legendPosition |
Position of legend ('top', 'bottom', 'left', 'right', 'none'). |
legendLabSize |
Size of plot legend text. |
legendTitleSize |
Size of plot legend title text. |
legendIconSize |
Size of plot legend icons / symbols. |
encircle |
Logical, indicating whether to draw a polygon around the groups specified by 'colby'. |
encircleFill |
Logical, if 'encircle == TRUE', this determines whether to fill the encircled region or not. |
encircleFillKey |
Vector of name-value pairs relating to value passed to 'encircleFill', e.g., c(A='forestgreen', B='gold'). If NULL, the fill is controlled by whatever has already been used for 'colby' / 'colkey'. |
encircleAlpha |
Alpha for purposes of controlling colour transparency of the encircled region. Used when 'encircle == TRUE'. |
encircleLineSize |
Line width of the encircled line when 'encircle == TRUE'. |
encircleLineCol |
Colour of the encircled line when 'encircle == TRUE'. |
ellipse |
Logical, indicating whether to draw a data ellipse around the groups specified by 'colby'. |
ellipseType |
[paraphrased from https://ggplot2.tidyverse.org/reference/stat_ellipse.html] The type of ellipse. "t" assumes a multivariate t-distribution, while "norm" assumes a multivariate normal distribution. "euclid" draws a circle with the radius equal to level, representing the euclidean distance from the center. This ellipse probably won't appear circular unless coord_fixed() is applied. |
ellipseLevel |
[paraphrased from https://ggplot2.tidyverse.org/reference/stat_ellipse.html] The level at which to draw an ellipse, or, if ellipseType="euclid", the radius of the circle to be drawn. |
ellipseSegments |
[from https://ggplot2.tidyverse.org/reference/stat_ellipse.html] The number of segments to be used in drawing the ellipse. |
ellipseFill |
Logical, if 'ellipse == TRUE', this determines whether to fill the region or not. |
ellipseFillKey |
Vector of name-value pairs relating to value passed to 'ellipseFill', e.g., c(A='forestgreen', B='gold'). If NULL, the fill is controlled by whatever has already been used for 'colby' / 'colkey'. |
ellipseAlpha |
Alpha for purposes of controlling colour transparency of the ellipse region. Used when 'ellipse == TRUE'. |
ellipseLineSize |
Line width of the ellipse line when 'ellipse == TRUE'. |
ellipseLineCol |
Colour of the ellipse line when 'ellipse == TRUE'. |
xlim |
Limits of the x-axis. |
ylim |
Limits of the y-axis. |
lab |
A vector containing labels to add to the plot. |
labSize |
Size of labels. |
boxedLabels |
Logical, draw text labels in boxes. |
selectLab |
A vector containing a subset of lab to plot. |
drawConnectors |
Logical, indicating whether or not to connect plot labels to their corresponding points by line connectors. |
widthConnectors |
Line width of connectors. |
colConnectors |
Line colour of connectors. |
max.overlaps |
Equivalent of max.overlaps in ggrepel. Set to 'Inf' to always display all labels when drawConnectors = TRUE. |
maxoverlapsConnectors |
See max.overlaps. |
min.segment.length |
When drawConnectors = TRUE, specifies the minimum length of the connector line segments. |
directionConnectors |
direction in which to draw connectors. 'both', 'x', or 'y'. |
xlab |
Label for x-axis. |
xlabAngle |
Rotation angle of x-axis labels. |
xlabhjust |
Horizontal adjustment of x-axis labels. |
xlabvjust |
Vertical adjustment of x-axis labels. |
ylab |
Label for y-axis. |
ylabAngle |
Rotation angle of y-axis labels. |
ylabhjust |
Horizontal adjustment of y-axis labels. |
ylabvjust |
Vertical adjustment of y-axis labels. |
axisLabSize |
Size of x- and y-axis labels. |
title |
Plot title. |
subtitle |
Plot subtitle. |
caption |
Plot caption. |
titleLabSize |
Size of plot title. |
subtitleLabSize |
Size of plot subtitle. |
captionLabSize |
Size of plot caption. |
hline |
Draw one or more horizontal lines passing through this/these values on y-axis. For single values, only a single numerical value is necessary. For multiple lines, pass these as a vector, e.g., c(60,90). |
hlineType |
Line type for hline ('blank', 'solid', 'dashed', 'dotted', 'dotdash', 'longdash', 'twodash'). |
hlineCol |
Colour of hline. |
hlineWidth |
Width of hline. |
vline |
Draw one or more vertical lines passing through this/these values on x-axis. For single values, only a single numerical value is necessary. For multiple lines, pass these as a vector, e.g., c(60,90). |
vlineType |
Line type for vline ('blank', 'solid', 'dashed', 'dotted', 'dotdash', 'longdash', 'twodash'). |
vlineCol |
Colour of vline. |
vlineWidth |
Width of vline. |
gridlines.major |
Logical, indicating whether or not to draw major gridlines. |
gridlines.minor |
Logical, indicating whether or not to draw minor gridlines. |
borderWidth |
Width of the border on the x and y axes. |
borderColour |
Colour of the border on the x and y axes. |
returnPlot |
Logical, indicating whether or not to return the plot object. |
Draw a bi-plot, comparing 2 selected principal components / eigenvectors.
A ggplot2
object.
Kevin Blighe <kevin@clinicalbioinformatics.co.uk>
options(scipen=10) options(digits=6) col <- 20 row <- 20000 mat1 <- matrix( rexp(col*row, rate = 0.1), ncol = col) rownames(mat1) <- paste0('gene', 1:nrow(mat1)) colnames(mat1) <- paste0('sample', 1:ncol(mat1)) mat2 <- matrix( rexp(col*row, rate = 0.1), ncol = col) rownames(mat2) <- paste0('gene', 1:nrow(mat2)) colnames(mat2) <- paste0('sample', (ncol(mat1)+1):(ncol(mat1)+ncol(mat2))) mat <- cbind(mat1, mat2) metadata <- data.frame(row.names = colnames(mat)) metadata$Group <- rep(NA, ncol(mat)) metadata$Group[seq(1,40,2)] <- 'A' metadata$Group[seq(2,40,2)] <- 'B' metadata$CRP <- sample.int(100, size=ncol(mat), replace=TRUE) metadata$ESR <- sample.int(100, size=ncol(mat), replace=TRUE) p <- pca(mat, metadata = metadata, removeVar = 0.1) biplot(p) biplot(p, colby = 'Group', shape = 'Group') biplot(p, colby = 'Group', colkey = c(A = 'forestgreen', B = 'gold'), legendPosition = 'right') biplot(p, colby = 'Group', colkey = c(A='forestgreen', B='gold'), shape = 'Group', shapekey = c(A=10, B=21), legendPosition = 'bottom')