This function facilitates structure plots with options that resemble those of plot_popkin() in name and results.
The biggest difference is this function plots single panels (technically 2 panels including the legend, unless it is omitted), whereas plot_popkin() can plot multiple kinship matrices with a shared legend.
plot_admix(
Q,
col = RColorBrewer::brewer.pal(max(ncol(Q), 3), "Paired"),
mar_pad = 0.2,
panel_letters = NA,
panel_letters_cex = 1.5,
panel_letters_adj = -0.1,
axis_lab_cex = 1,
xlab = "Individuals",
xlab_line = 1,
xlab_cex = axis_lab_cex,
ylab = "Ancestry",
ylab_line = 2,
ylab_side = 2,
ylab_cex = axis_lab_cex,
leg_title = "Ancestries",
leg_title_cex = axis_lab_cex,
leg_cex = 1,
leg_mar = 3,
leg_width = 0.2,
leg_omit = FALSE,
layout_add = !leg_omit,
names = FALSE,
names_cex = 1,
names_line = NA,
names_las = 2,
labs = NULL,
labs_cex = 1,
labs_las = 0,
labs_line = 0,
labs_sep = TRUE,
labs_lwd = 1,
labs_col = "black",
labs_ticks = FALSE,
labs_text = TRUE,
labs_even = FALSE,
...
)The admixture proportions matrix, with n individuals along rows and K ancestries along columns.
Rows should sum to 1, but this is not enforced.
There must be at least 2 ancestries.
The ancestry labels used by the legend must be the column names, which are unlabeled if the column names are missing.
A vector of at least K colors for the ancestries (extra colors are ignored).
By default uses the "Paired" palette of RColorBrewer, which has at most 12 colors, so please provide colors if K > 12.
Since the minimum number of colors for "Paired" is 3, when K = 2 we ask for 3 colors, then remove the middle color internally.
Margin padding used for legend panel only (margins for first/main panel are not altered by this function).
Panel letter to include in first/main panel (default NA is no letter).
Despite name (matches plot_popkin()), must be scalar.
Scaling factor of panel letter (default 1.5).
X-axis adjustment for panel letter (default -0.1). Negative values place the letter into the left margin area. Might need adjustment depending on the size of the left margin.
AXIS LABEL OPTIONS
Scaling factor for x-axis, y-axis, and legend title labels (which can also be set individually, see below).
X-axis label (default "Individuals").
Set to NA to omit.
The value of line for xlab passed to graphics::mtext().
Scaling factor for x-axis label.
Y-axis label (default "Ancestry").
Set to NA to omit.
The value of line for ylab passed to graphics::mtext().
The value of side for ylab passed to graphics::mtext() (2 is y-axis, 1 is x-axis, can also place on top (3) or right (4)).
Scaling factor for y-axis label.
LEGEND (COLOR KEY) OPTIONS
The name of the categorical ancestry variable (default "Ancestries").
Scaling factor for legend title label.
Scaling factor for ancestry labels.
Margin values for the kinship legend panel only.
A length-4 vector (in c( bottom, left, top, right ) format that graphics::par() 'mar' expects) specifies the full margins, to which mar_pad is added.
Otherwise, the margins used in the last panel are preserved with the exception that the left margin is set to mar_pad, and if leg_mar is length-1, it is added to mar_pad to specify the right margin.
The width of the legend panel, relative to the width of the main panel.
This value is passed to graphics::layout() (ignored if layout_add = FALSE).
If TRUE, no legend (second panel) is produced (default FALSE is to include legend).
If TRUE (default) then graphics::layout() is called internally to create two panels: the main panel and the color key legend.
The original layout is reset when plotting is complete and if layout_add = TRUE.
If a non-standard layout or additional panels (beyond those provided by this function) are desired, set to FALSE and call graphics::layout() yourself beforehand.
INDIVIDUAL LABEL OPTIONS
If TRUE, the row (individual) names are plotted in the structure barplot.
Scaling factor for the individual names.
Line where individual names are placed.
Orientation of labels relative to axis. Default (2) makes labels perpendicular to axis.
SUBPOPULATION LABEL OPTIONS
Subpopulation labels for individuals in the admixture matrix. Use a matrix of labels to show groupings at more than one level (for a hierarchy or otherwise).
A vector of label scaling factors for each level of labs.
A vector of label orientations (in format that graphics::mtext() expects) for each level of labs.
A vector of lines where labels are placed (in format that graphics::mtext() expects) for each level of labs.
A vector of logicals that specify whether lines separating the subpopulations are drawn for each level of labs.
A vector of line widths for the lines that divide subpopulations (if labs_sep = TRUE) for each level of labs.
A vector of colors for the lines that divide subpopulations (if labs_sep = TRUE) for each level of labs.
A vector of logicals that specify whether ticks separating the subpopulations are drawn for each level of labs.
A vector of logicals that specify whether the subpopulation labels are shown for each level of labs. Useful for including separating lines or ticks without text.
A vector of logicals that specify whether the subpopulations labels are drawn with equal spacing for each level of labs.
When TRUE, lines mapping the equally-spaced labels to the unequally-spaced subsections of the heatmap are also drawn.
Additional options passed to graphics::barplot().
# create random proportions for two ancestries
Q <- runif( 10 )
Q <- cbind( Q, 1 - Q )
# add ancestry names
colnames( Q ) <- c('A1', 'A2')
# plot this data!
plot_admix( Q )
# See vignette for more elaborate examples!
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