pairsplot {PCAtools} | R Documentation |
Draw multiple bi-plots.
pairsplot(pcaobj, components = getComponents(pcaobj, seq_len(5)), triangle = TRUE, trianglelabSize = 18, plotaxes = TRUE, margingaps = unit(c(0.1, 0.1, 0.1, 0.1), 'cm'), ncol = NULL, nrow = NULL, x = NULL, y = NULL, colby = NULL, colkey = NULL, singlecol = NULL, shape = NULL, shapekey = NULL, pointSize = 1.0, legendPosition = 'none', legendLabSize = 6, legendIconSize = 1.5, xlim = NULL, ylim = NULL, lab = FALSE, labSize = 1.5, labhjust = 1.5, labvjust = 0, selectLab = NULL, drawConnectors = FALSE, widthConnectors = 0.5, colConnectors = 'grey50', xlab = NULL, xlabAngle = 0, xlabhjust = 0.5, xlabvjust = 0.5, ylab = NULL, ylabAngle = 0, ylabhjust = 0.5, ylabvjust = 0.5, axisLabSize = 10, title = NULL, titleLabSize = 32, 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(). REQUIRED. |
components |
The principal components to be included in the plot. These will be compared in a pairwise fashion via multiple calls to biplot(). DEFAULT = getComponents(pcaobj, seq_len(5)). OPTIONAL. |
triangle |
Logical, indicating whether or not to draw the plots in the upper panel in a triangular arrangement? Principal component names will be labeled along the diagonal. DEFAULT = TRUE. OPTIONAL. |
trianglelabSize |
Size of p rincipal component label (when triangle = TRUE). DEFAULT = 18. OPTIONAL. |
plotaxes |
Logical, indicating whether or not to draw the axis tick, labels, and titles. DEFAULT = TRUE. OPTIONAL. |
margingaps |
The margins between plots in the plot space. Takes the form of a 'unit()' variable. DEFAULT = unit(c(0.1, 0.1, 0.1, 0.1), 'cm'). OPTIONAL. |
ncol |
If triangle = FALSE, the number of columns in the final merged plot. DEFAULT = NULL. OPTIONAL. |
nrow |
If triangle = FALSE, the number of rows in the final merged plot. DEFAULT = NULL. OPTIONAL. |
x |
A principal component to plot on x-axis. All principal component names are stored in pcaobj$label. DEFAULT = NULL. OPTIONAL. |
y |
A principal component to plot on y-axis. All principal component names are stored in pcaobj$label. DEFAULT = NULL. OPTIONAL. |
colby |
If NULL, all points will be coloured differently. If not NULL, value is assumed to be a column name in pcaobj$metadata relating to some grouping/categorical variable. DEFAULT = NULL. OPTIONAL. |
colkey |
Vector of name-value pairs relating to value passed to 'col', e.g., c(A='forestgreen', B='gold'). DEFAULT = NULL. OPTIONAL. |
singlecol |
If specified, all points will be shaded by this colour. Overrides 'col'. DEFAULT = NULL. OPTIONAL. |
shape |
If NULL, all points will be have the same shape. If not NULL, value is assumed to be a column name in pcaobj$metadata relating to some grouping/categorical variable. DEFAULT = NULL. OPTIONAL. |
shapekey |
Vector of name-value pairs relating to value passed to 'shape', e.g., c(A=10, B=21). DEFAULT = NULL. OPTIONAL. |
pointSize |
Size of plotted points. DEFAULT = 1.0. OPTIONAL. |
legendPosition |
Position of legend ('top', 'bottom', 'left', 'right', 'none'). DEFAULT = 'none'. OPTIONAL. |
legendLabSize |
Size of plot legend text. DEFAULT = 6. OPTIONAL. |
legendIconSize |
Size of plot legend icons / symbols. DEFAULT = 1.5. OPTIONAL. |
xlim |
Limits of the x-axis. DEFAULT = NULL. OPTIONAL. |
ylim |
Limits of the y-axis. DEFAULT = NULL. OPTIONAL. |
lab |
Logical, indicating whether or not to label the points in the plot space. Labels will be taken as the original colnames of the input object, usually sample IDs. DEFAULT = FALSE. OPTIONAL. |
labSize |
Size of labels. DEFAULT = 1.5. OPTIONAL. |
labhjust |
Horizontal adjustment of label. DEFAULT = 1.5. OPTIONAL. |
labvjust |
Vertical adjustment of label. DEFAULT = 0. OPTIONAL. |
selectLab |
A vector containing a subset of lab to plot. DEFAULT = NULL. OPTIONAL. |
drawConnectors |
Logical, indicating whether or not to connect plot labels to their corresponding points by line connectors. DEFAULT = FALSE. OPTIONAL. |
widthConnectors |
Line width of connectors. DEFAULT = 0.5. OPTIONAL. |
colConnectors |
Line colour of connectors. DEFAULT = 'grey50'. OPTIONAL. |
xlab |
Label for x-axis. DEFAULT = NULL. OPTIONAL. |
xlabAngle |
Rotation angle of x-axis labels. DEFAULT = 0. OPTIONAL. |
xlabhjust |
Horizontal adjustment of x-axis labels. DEFAULT = 0.5. OPTIONAL. |
xlabvjust |
Vertical adjustment of x-axis labels. DEFAULT = 0.5. OPTIONAL. |
ylab |
Label for y-axis. DEFAULT = NULL. OPTIONAL. |
ylabAngle |
Rotation angle of y-axis labels. DEFAULT = 0. OPTIONAL. |
ylabhjust |
Horizontal adjustment of y-axis labels. DEFAULT = 0.5. OPTIONAL. |
ylabvjust |
Vertical adjustment of y-axis labels. DEFAULT = 0.5. OPTIONAL. |
axisLabSize |
Size of x- and y-axis labels. DEFAULT = 10. OPTIONAL. |
title |
Plot title. DEFAULT = NULL. OPTIONAL. |
titleLabSize |
Size of plot title. DEFAULT = 32. OPTIONAL. |
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). DEFAULT = NULL. OPTIONAL. |
hlineType |
Line type for hline ('blank', 'solid', 'dashed', 'dotted', 'dotdash', 'longdash', 'twodash'). DEFAULT = 'longdash'. OPTIONAL. |
hlineCol |
Colour of hline. DEFAULT = 'black'. OPTIONAL. |
hlineWidth |
Width of hline. DEFAULT = 0.4. OPTIONAL. |
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). DEFAULT = NULL. OPTIONAL. |
vlineType |
Line type for vline ('blank', 'solid', 'dashed', 'dotted', 'dotdash', 'longdash', 'twodash'). DEFAULT = 'longdash'. OPTIONAL. |
vlineCol |
Colour of vline. DEFAULT = 'black'. OPTIONAL. |
vlineWidth |
Width of vline. DEFAULT = 0.4. OPTIONAL. |
gridlines.major |
Logical, indicating whether or not to draw major gridlines. DEFAULT = TRUE. OPTIONAL. |
gridlines.minor |
Logical, indicating whether or not to draw minor gridlines. DEFAULT = TRUE. OPTIONAL. |
borderWidth |
Width of the border on the x and y axes. DEFAULT = 0.8. OPTIONAL. |
borderColour |
Colour of the border on the x and y axes. DEFAULT = 'black'. OPTIONAL. |
returnPlot |
Logical, indicating whether or not to return the plot object. DEFAULT = TRUE. OPTIONAL. |
A cowplot
object.
Kevin Blighe <kevin@clinicalbioinformatics.co.uk>, Myles Lewis <myles.lewis@qmul.ac.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) pairsplot(p, triangle = TRUE)