Examples
Several simple use examples are given in the help for each of the layer and other functions exported by package ‘ggpmisc’. Here we give additional examples, mostly more advanced, together with brief explanations.
Statistics
stat_correlation()
The statistic stat_correlation() computes one of
Pearson, Kendall or Spearman correlation coefficients and tests if they
differ from zero. This is done by calling
stats::cor.test(), with all of its formal parameters
supported. Depending on the argument passed to parameter
output.type the values returned very. The default behaviour
is to generate labels as character strings using R’s expression
syntax, suitable to be parsed. This ggplot statistic can also
output labels using other mark-up languages, including \(\LaTeX\) and Markdown, or just numeric
values. Nevertheless, all examples below use expression syntax, which is
the most commonly used.
We first generate a set of artificial data suitable for the plotting examples in this and subsequent sections.
set.seed(4321)
x <- (1:100) / 10
y <- x + rnorm(length(x))
my.data <- data.frame(x = x,
y = y,
y.desc = - y,
group = c("A", "B"))For the first example we use defaults to add an annotation with Pearson’s correlation coefficient.
Grouping is supported.
We can also compute Spearman’s rank correlation. (The symbol used for it is the letter rho to distinguish it from Pearson’s correlation for which R or r are used as symbols.)
Statistic stat_correlation() generates multiple labels
as listed in the tables above. We can combine them freely within a call
to aes() to customize the annotations, or we can use the
convenience function use_label() to create the mapping.
ggplot(my.data, aes(x, y, color = group)) +
geom_point() +
stat_correlation(mapping = use_label("R", "t", "P", "n"))
Facets are also supported.
Using the numeric values returned it is possible to set other aesthetics on-the-fly.
ggplot(my.data, aes(x, y)) +
geom_point() +
stat_correlation(mapping = aes(color = ifelse(after_stat(cor) > 0.955,
"red", "black"))) +
scale_color_identity() +
facet_wrap(~group)
Above we use the value of the correlation coefficient, but other
numeric values such as p.value can be used similarly. In
addition to colour, any aesthetics recognized by the geometry used such
as alpha and face can be also mapped. The
statistics described below for adding equations of the fitted models
have user interfaces very similar to that of
stat_correaltion() so examples can be easily adapted.
Please, see the next section for examples of the use of different
geometries instead of the default one, and other advanced examples.
stat_poly_eq() and stat_poly_line()
A frequently used annotation in plots showing fitted lines is the
display of the parameters estimates from the model fit as an equation.
stat_poly_eq() automates this for models of y on
x or x on y fitted with function
lm(), and MASS:rlm() or a user-supplied model
fitting function and arguments. By default this statistic
behaves similarly as ggplot2::stat_smooth() with
method = "lm" for y on x fits but adds
support for model formulas of x on y (in addition to
the use of orientation = "y"). Its default behaviour is to
generate labels as character strings using R’s expression
syntax. This statistic can also output equations using different mark-up
languages, including \(\LaTeX\) and
Markdown, or just numeric values selected by the argument passed to
parameter output.type. Nevertheless, all examples below use
R’s expression syntax.
The statistic stat_poly_line() adds a layer nearly
identical to that from ggplot2::stat_smooth() but has the
same user interface and default arguments as
stat_poly_eq().
We first generate a set of artificial data suitable for the plotting examples.
set.seed(4321)
# generate artificial data
x <- 1:100
y <- (x + x^2 + x^3) + rnorm(length(x), mean = 0, sd = mean(x^3) / 4)
y <- y / max(y)
my.data <- data.frame(x,
y,
group = c("A", "B"),
y2 = y * c(1, 2) + c(0, 0.2),
block = c("a", "a", "b", "b"),
wt = sqrt(x))First, one example using defaults except for the model
formula. The best practice, ensuring that the formula used
in both statistics is the same is to assign the formula to a
variable, as shown here. This is because the same model is fit twice to
the same data, once in stat_poly_line() and
once in stat_poly_eq().
We can write the model formula for a polynomial explicitly or using
function poly(). When using function poly() it
is in most cases necessary to set raw = TRUE as the default
is to use orthogonal polynomials which although fitting the same line
will have different estimates for the coefficients than those in the
usual raw polynomials.
formula <- y ~ poly(x, 3, raw = TRUE)
ggplot(my.data, aes(x, y)) +
geom_point() +
stat_poly_line(formula = formula) +
stat_poly_eq(formula = formula)
A ready formatted equation is also returned as a string that needs to
be parsed into an expression for display. Function
use_label() can be used to select or assemble the
expression and map it to the label aesthetic. The default
separator is suitable for labels to be parsed into R expressions, but
this default can be over-ridden by passing an argument to parameter
sep. In this example we select the fitted model equation
using key "eq" as argument to use_label()
.
formula <- y ~ poly(x, 3, raw = TRUE)
ggplot(my.data, aes(x, y)) +
geom_point() +
stat_poly_line(formula = formula) +
stat_poly_eq(mapping = use_label("eq"), formula = formula)
The mapping can also be done with ggplot2::aes() using
the name of the variable in the returned data containing
the desired label and enclosing it in ggplot2::after_stat()
to signal that it is a variable returned by the statistic.
formula <- y ~ poly(x, 3, raw = TRUE)
ggplot(my.data, aes(x, y)) +
geom_point() +
stat_poly_line(formula = formula) +
stat_poly_eq(mapping = aes(label = after_stat(eq.label)),
formula = formula)
stat_poly_eq() makes available several character strings
in the returned data frame in separate columns: eq.label,
rr.label, adj.rr.label,
AIC.label, BIC.label,
f.value.label, p.value.label and
n. One of these, rr.label, is used by default,
but use_label() and aes() together with
after_stat() can be used to map a different one to the
label aesthetic. Here we show the adjusted coefficient of
determination, \(R^2_\mathrm{adj}\),
Akaike’s information criterion, AIC. We call stat_poly_eq()
twice to be able to separately control the position and size of each
label. As parameter mapping is the first one in the
statistics, we can pass the mapping by position (without writing
mapping =).
formula <- y ~ poly(x, 3, raw = TRUE)
ggplot(my.data, aes(x, y)) +
geom_point() +
stat_poly_line(formula = formula) +
stat_poly_eq(mapping = use_label("adj.R2"), formula = formula) +
stat_poly_eq(mapping = use_label("AIC"), label.x = "right", label.y = "bottom", size = 3,
formula = formula)
Within ggplot2::aes() it is also possible to
compute new labels based on those returned plus “arbitrary”
text. The labels returned by default are meant to be parsed
into expressions, so any text added should be valid for a string that
will be parsed. Inserting a comma plus white space in an expression
requires some trickery in the argument passed to parameter
sep of paste(), or use_label().
Do note the need to escape the embedded quotation marks as
\". Combining the labels in this way ensures correct
alignment. To insert only white space sep = "~~~~~" can be
used, with each tilde character, ~, adding a rather small
amount of white space. We show here how to change the axis labels to
ensure consistency with the typesetting of the equation.
formula <- y ~ poly(x, 3, raw = TRUE)
ggplot(my.data, aes(x, y)) +
geom_point() +
stat_poly_line(formula = formula) +
stat_poly_eq(mapping = use_label("eq", "adj.R2"),
formula = formula) +
labs(x = expression(italic(x)), y = expression(italic(y)))
Above we combined two character-string labels, but it is possible to
add additional ones and even character strings constants. In the next
example we use several labels instead of just two, and separate them
with various character strings. In this case we need to use
paste() and ggplot2::aes() as
use_label() uses a single value for sep. We
also change the size of the text in the label.
formula <- y ~ poly(x, 3, raw = TRUE)
ggplot(my.data, aes(x, y)) +
geom_point() +
stat_poly_line(formula = formula) +
stat_poly_eq(aes(label = paste(after_stat(eq.label), "*\" with \"*",
after_stat(rr.label), "*\", \"*",
after_stat(f.value.label), "*\", and \"*",
after_stat(p.value.label), "*\".\"",
sep = "")),
formula = formula, size = 3)
It is also possible to format the text using plain(),
italic(), bold() or bolditalic()
an other commands as described in the help entry for
plotmath.
formula <- y ~ poly(x, 3, raw = TRUE)
ggplot(my.data, aes(x, y)) +
geom_point() +
stat_poly_line(formula = formula) +
stat_poly_eq(mapping = use_label("eq", "adj.R2", sep = "~~italic(\"with\")~~"),
formula = formula)
As these are expressions, to include two lines of text, we need
either to add stat_poly_eq() twice, passing an argument to
label.y to reposition one of the labels (as shown above) or
use (as shown here) atop() within the expression to create
a single label with two lines of text.
formula <- y ~ poly(x, 3, raw = TRUE)
ggplot(my.data, aes(x, y)) +
geom_point() +
stat_poly_line(formula = formula) +
stat_poly_eq(aes(label = paste("atop(", after_stat(AIC.label), ",",
after_stat(BIC.label), ")", sep = "")),
formula = formula)
Next, one example of how to remove the left hand side (lhs).
formula <- y ~ poly(x, 3, raw = TRUE)
ggplot(my.data, aes(x, y)) +
geom_point() +
stat_poly_line(formula = formula) +
stat_poly_eq(mapping = use_label("eq"),
eq.with.lhs = FALSE,
formula = formula)
Replacing the lhs.
formula <- y ~ poly(x, 3, raw = TRUE)
ggplot(my.data, aes(x, y)) +
geom_point() +
stat_poly_line(formula = formula) +
stat_poly_eq(mapping = use_label("eq"),
eq.with.lhs = "italic(hat(y))~`=`~",
formula = formula)
Replacing both the lhs and the variable symbol used on the rhs.
formula <- y ~ poly(x, 3, raw = TRUE)
ggplot(my.data, aes(x, y)) +
geom_point() +
stat_poly_line(formula = formula) +
stat_poly_eq(mapping = use_label("eq", "R2"),
eq.with.lhs = "italic(h)~`=`~",
eq.x.rhs = "~italic(z)",
formula = formula) +
labs(x = expression(italic(z)), y = expression(italic(h)))
As any valid R expression can be used, Greek letters are also supported, as well as the inclusion in the label of variable transformations used in the model formula or applied to the data. In addition, in the next example we insert white space in between the parameter estimates and the variable symbol in the equation.
formula <- y ~ poly(x, 2, raw = TRUE)
ggplot(my.data, aes(x, log10(y + 1e6))) +
geom_point() +
stat_poly_line(formula = formula) +
stat_poly_eq(mapping = use_label("eq"),
eq.with.lhs = "plain(log)[10](italic(delta)+10^6)~`=`~",
eq.x.rhs = "~Omega",
formula = formula) +
labs(y = expression(plain(log)[10](italic(delta)+10^6)), x = expression(Omega))
Examples of polynomials of different orders, and fits through the
origin. A degree 1 polynomial is linear regression with
formula = y ~ x, which is the default. Linear regression
through the origin is supported by passing
formula = y ~ x - 1, or formula = y ~ x + 0.
High order polynomials are most easily requested using
poly() in the model formula, as shown next.
formula <- y ~ poly(x, 5, raw = TRUE)
ggplot(my.data, aes(x, y)) +
geom_point() +
stat_poly_line(formula = formula) +
stat_poly_eq(mapping = use_label("eq"), formula = formula)
Intercept forced to zero for a third degree polynomial defined
explicitly, as this case is not supported by poly().
formula <- y ~ x + I(x^2) + I(x^3) - 1
ggplot(my.data, aes(x, y)) +
geom_point() +
stat_poly_line(formula = formula) +
stat_poly_eq(aes(label = after_stat(eq.label)), formula = formula)
Even when labels are returned, numeric values are also returned for
r.squared, adj.r.squared, p.value
and n. This can be used in ggplot2::aes() for
example to show the equation only if a certain condition like a minimum
value for r.square or p.value has been
reached.
formula <- y ~ poly(x, 3, raw = TRUE)
ggplot(my.data, aes(x, y)) +
geom_point() +
stat_poly_line(formula = formula) +
stat_poly_eq(aes(label = ifelse(after_stat(adj.r.squared > 0.3),
paste(after_stat(eq.label), after_stat(adj.rr.label),
sep = "*\", \"*"),
after_stat(adj.rr.label))),
formula = formula) +
labs(x = expression(italic(x)), y = expression(italic(y)))
Fitting different models to different panels is supported.
User-defined method functions are required to return an object that
inherits from class "lm". The function is applied per group
and panel, and the model formula fitted can differ among
them, as it is retrieved from this object to construct the equation
label.
In the example below instead of using stats::lm() as
method, we define a wrapper function that tests for the significance of
the slope in linear regression, and if not significant, fits the mean
instead.
poly_or_mean <- function(formula, data, ...) {
fm <- lm(formula = formula, data = data, ...)
if (anova(fm)[["Pr(>F)"]][1] > 0.1) {
lm(formula = y ~ 1, data = data, ...)
} else {
fm
}
}We then use our function poly_or_mean() as the
method.
ggplot(mpg, aes(displ, hwy)) +
geom_point() +
stat_poly_line(method = "poly_or_mean") +
stat_poly_eq(method = poly_or_mean,
aes(label = after_stat(eq.label)),
label.x = "right") +
theme(legend.position = "bottom") +
facet_wrap(~class, ncol = 2)
We give below several examples to demonstrate how other components of
the ggplot object affect the behaviour of this
statistic.
Facets work as expected both with fixed or free scales. Although below we had to adjust the size of the font used for the equation.
formula <- y ~ poly(x, 3, raw = TRUE)
ggplot(my.data, aes(x, y2)) +
geom_point() +
stat_poly_line(formula = formula) +
stat_poly_eq(aes(label = after_stat(eq.label)), size = 3,
formula = formula) +
facet_wrap(~group)
formula <- y ~ poly(x, 3, raw = TRUE)
ggplot(my.data, aes(x, y2)) +
geom_point() +
stat_poly_line(formula = formula) +
stat_poly_eq(aes(label = after_stat(eq.label)), size = 3,
formula = formula) +
facet_wrap(~group, scales = "free_y")
Grouping works as expected. In this example we create groups
using the colour aesthetic, but factors or discrete variables mapped to
other aesthetics including the “invisible” group aesthetic.
We can use justification and supply an absolute location for the
equation, but the default frequently works well as in the example
below.
formula <- y ~ poly(x, 3, raw = TRUE)
ggplot(my.data, aes(x, y2, colour = group)) +
geom_point() +
stat_poly_line(formula = formula) +
stat_poly_eq(aes(label = after_stat(eq.label)), formula = formula, vstep = 0.06)
To add a label to the equation for each group, we map it to a
pseudo-aesthetic named grp.label.
formula <- y ~ poly(x, 3, raw = TRUE)
ggplot(my.data, aes(x, y2, colour = group, grp.label = group)) +
geom_point() +
stat_poly_line(formula = formula) +
stat_poly_eq(aes(label = after_stat(paste("bold(", grp.label, "*\":\")~~",
eq.label, sep = ""))),
formula = formula)
Being able to label equations allows us to dispense with the use of colour, which in some cases is needed for publication in journals and books.
formula <- y ~ poly(x, 3, raw = TRUE)
ggplot(my.data, aes(x, y2, linetype = group, grp.label = group)) +
geom_point() +
stat_poly_line(formula = formula, color = "black") +
stat_poly_eq(aes(label = after_stat(paste("bold(", grp.label, "*':')~~~",
eq.label, sep = ""))),
formula = formula)
User supplied label positions relative to the ranges of the
x and y scales are also supported, both through string
constants and numeric values in the range 0 to 1, when using the default
ggpp::geom_text_npc().
formula <- y ~ poly(x, 3, raw = TRUE)
ggplot(my.data, aes(x, y2, colour = group)) +
geom_point() +
stat_poly_line(formula = formula) +
stat_poly_eq(aes(label = after_stat(eq.label)),
formula = formula,
label.x = "centre")
The default locations are based on normalized coordinates, and consequently these defaults work even when the range of the x and y scales varies from panel to panel.
formula <- y ~ poly(x, 3, raw = TRUE)
ggplot(my.data, aes(x, y2, fill = block)) +
geom_point(shape = 21, size = 3) +
stat_poly_line(formula = formula) +
stat_poly_eq(aes(label = after_stat(rr.label)), size = 3,
geom = "label_npc", alpha = 0.33,
formula = formula) +
facet_wrap(~group, scales = "free_y")
If grouping is not the same within each panel created by faceting,
i.e., not all groups have data in all panels, the automatic location of
labels results in “holes” for the factor levels not present in a given
panel. This behaviour ensures consistent positioning of labels for the
same groups across panels. If positioning that leaves no gaps is
desired, it is possible to explicitly pass as argument the positions for
each individual label. In the plot below the simultaneous mapping to
both colour and fill aesthetics creates four groups, two with data in
panel A and the other two in panel B, but the vector passed as argument
to label.y determines the y position (in
npc units) four each of the four labels.
formula <- y ~ poly(x, 3, raw = TRUE)
ggplot(my.data, aes(x, y2, colour = group, fill = block)) +
geom_point(shape = 21, size = 3) +
stat_poly_line(formula = formula) +
stat_poly_eq(aes(label = after_stat(rr.label)), size = 3, alpha = 0.2,
geom = "label_npc", label.y = c(0.95, 0.85, 0.95, 0.85),
formula = formula) +
facet_wrap(~group, scales = "free_y")
It is possible to use ggplot2::geom_text() and
ggplot2::geom_label() instead of the default
ggpp::geom_text_npc() (or
ggpp::geom_label_npc()) but in this case, if label
coordinates are given explicitly they should be expressed in native data
coordinates. When multiple labels need to be positioned a vector of
coordinates can be used as shown here for label.x and
label.y.
formula <- y ~ poly(x, 3, raw = TRUE)
ggplot(my.data, aes(x, y2, colour = group)) +
geom_point() +
stat_poly_line(formula = formula) +
stat_poly_eq(geom = "text", aes(label = after_stat(eq.label)),
label.x = c(100, 20), label.y = c(-0.1, 2.1), hjust = "inward",
formula = formula)
Note: Automatic positioning using
ggplot2::geom_text() and ggplot2::geom_label()
is supported except when faceting uses free scales. In this case
ggpp::geom_text_npc() and/or
ggpp::geom_label_npc() or positions supplied by the user
must be used.
Occasionally, possibly as a demonstration in teaching, we may want to compare a fit of x on y and one of y on x in the same plot. Here, this example also serves as introduction to the next section, which describes the use of major axis regression or Model II regression.
As is the case for model fitting functions themselves, which variable
is dependent (response) and which is independent (explanatory) is simply
indicated by the model equation passed as argument to
formula, or consistently with
ggplot2::stat_smooth() through parameter
orientation as show below.
ggplot(my.data, aes(x, y)) +
geom_point() +
stat_poly_line(formula = y ~ x, color = "blue") +
stat_poly_eq(mapping = use_label("R2", "eq"), color = "blue") +
stat_poly_line(formula = y ~ x, color = "red", orientation = "y") +
stat_poly_eq(mapping = use_label("R2", "eq"), color = "red", orientation = "y",
label.y = 0.9)
stat_ma_eq() and stat_ma_line()
Package ‘lmodel2’ implements Model II fits for major axis (MA), standard major axis (SMA) and ranged major axis (RMA) regression for linear relationships. These approaches of regression are used when both variables are subject to random variation and the intention is not to estimate y from x but instead to describe the slope of the relationship between them. A typical example in biology are allometric relationships. Rather frequently, OLS linear model fits are used in cases where Model II regression would be preferable.
In the figure above we see that the ordinary least squares (OLS) linear regression of y on x and x on y differ. Major axis regression provides an estimate of the slope that is independent of the direction of the relationship relation. \(R^2\) remains the same in all cases, and with major axis regression while the coefficient estimates in the equation change, they correspond to exactly the same line.
ggplot(my.data, aes(x, y)) +
geom_point() +
stat_ma_line(color = "blue") +
stat_ma_eq(mapping = use_label("R2", "eq"), color = "blue") +
stat_ma_line(color = "red", orientation = "y") +
stat_ma_eq(mapping = use_label("R2", "eq"), color = "red", orientation = "y",
label.y = 0.9)
stat_quant_eq(), stat_quant_line() and stat_quant_band()
Package ‘quantreg’ implements quantile regression for multiple types
of models: linear models with function quantreg::rq(),
non-linear models with function quantreg::nlreg(), and
additive models with function quantreg::rqss(). Each of
these functions supports different methods of estimation which can be
passed through parameter method.args or more easily using a
character string such as "rq:br" argument to parameter
method of the statistic, where quantreg::rq()
is the model fit function and "br" the argument passed to
the method parameter of quantreg::rq(). As
with the statistics for polynomials described in the previous section,
all the statistics described in the current section support linear
models while stat_quant_line() and
stat_quant_band() also support additive models. (Support
for quantreg::nlreg() is not yet implemented.)
In the case of quantile regression it is frequently the case that
multiple quantile regressions are fitted. This case is not supported by
stat_poly_eq() and we need to use
stat_quant_eq(). This statistics is very similar to
stat_poly_eq() both in behaviour and parameters. It
supports quantile regression of y on x or x
on y fitted with function quantreg::rq.
The statistic stat_quant_line() adds a layer similar to
that created by ggplot2::stat_smooth() including confidence
bands for quantile regression, by default for p = 0.95.
However, it has the same user interface and default arguments as
stat_quant_eq(), and supports both x and
y as explanatory variable in formula and also
orientation. Confidence intervals for the fits to
individual quantiles fulfil the same purpose as in OLS fits: providing a
boundary for the estimated line computed for each individual
quantile. They are not shown by default, unless a single quantile is
passed as argument, but can be enabled with se = TRUE and
disabled with se = FALSE.
The statistic stat_quant_band() creates a line plus band
plot that is, by default equivalent to the box of a box plot showing
regressions as a band for quartiles plus a line for the median
regression. In this case, the band informs about the spread of the
observations in the same way as the box in box plots does.
Which three quantiles are fitted can be set through parameter
quantiles but in contrast to stat_quant_line()
and stat_quant_eq() only a vector of two or three quantiles
is accepted (with two quantiles the line is omitted and only a band
displayed).
Similarly to ggplot2::stat_quantiles(),
stat_quant_eq() and stat_quant_line() accept a
numeric vector as argument to quantiles and
output one equation or one line per group and quantile. Statistic
stat_quant_eq() also returns column grp.label
containing by default a character string indicating the value of the
quantile, and if a variable is mapped to the pseudo aesthetic
grp.label its value is prepended to the values of the
quantiles.
Here we use the default value for quantiles,
c(0.25, 0.50, 0.75), equivalent to those used for the box
of box plots, and we obtain a plot with a line for median regression and
a band highlighting the space between the quartiles.
Overriding the values for quantiles we find a boundary
containing 90% of the observations.
ggplot(my.data, aes(x, y)) +
geom_point() +
stat_quant_line(formula = y ~ poly(x, 2), quantiles = c(0.05, 0.95))
A line for the quantile regression plus a confidence band for it is
the default for a single quantile. (This is similar to the behaviour of
ggplot2::stat_smooth().)
ggplot(my.data, aes(x, y)) +
geom_point() +
stat_quant_line(formula = y ~ poly(x, 2), quantiles = 0.5)
With stat_quant_eq() we add the fitted equations to the
first example in this section (we also override the use of colour).
ggplot(my.data, aes(x, y)) +
geom_point() +
stat_quant_band(formula = formula, color = "black", fill = "grey60") +
stat_quant_eq(aes(label = paste(after_stat(qtl.label), "*\": \"*",
after_stat(eq.label), sep = "")),
formula = formula) +
theme_classic()
Grouping and faceting are supported by stat_quant_eq(),
stat_quant_line() and stat_quant_band(). Below
are some examples of grouping.
ggplot(my.data, aes(x, y, color = group)) +
geom_point() +
stat_quant_line(formula = formula) +
stat_quant_eq(aes(label = paste(after_stat(qtl.label), "*\": \"*",
after_stat(eq.label), sep = "")),
formula = formula)
Grouping can be combined with a group label by mapping in
aes() a character variable to grp.label.
ggplot(my.data, aes(x, y, group = group, linetype = group,
shape = group, grp.label = group)) +
geom_point() +
stat_quant_line(formula = formula, quantiles = c(0.05, 0.95), color = "black") +
stat_quant_eq(aes(label = paste(after_stat(grp.label), "*\", \"*",
after_stat(qtl.label), "*\": \"*",
after_stat(eq.label), sep = "")),
formula = formula, quantiles = c(0.05, 0.95)) +
theme_classic()
In some cases double quantile regression is an informative
method to assess reciprocal constraints. For this a fit of x on
y and one of y on x in the same plot are
computed for a large quantile. As is the case for model fitting
functions themselves this is simply indicated by the model passed as
argument to formula, or consistently with
ggplot2::stat_smooth() through parameter
orientation.
ggplot(my.data, aes(x, y)) +
geom_point() +
stat_quant_line(formula = y ~ x, color = "blue", quantiles = 0.05) +
stat_quant_eq(mapping = use_label("eq"), formula = y ~ x, color = "blue",
quantiles = 0.05) +
stat_quant_line(formula = x ~ y, color = "red", quantiles = 0.95) +
stat_quant_eq(mapping = use_label("eq"), formula = x ~ y, color = "red",
quantiles = 0.95, label.y = 0.9)
Please, see the section on stat_poly_eq() for additional
examples, as here we have highlighted mainly the differences between
these two statistics.
stat_multcomp
This section is still preliminary. Multiple comparisons are
frequently used when the effect of different levels of a factor are
individually of interest. Function stat_multcomp() computes
adjusted P-values for pairwise comparison using Tukey or Dunnet
contrasts using function glht() from package ‘multcomp’. To
complement the examples in the documentation of the function, we show
below examples that override several defaults.
Alternatives to the default “tag” values used to describe the
adjustment method can be obtained with arguments passed to parameter
adj.method.tag. In the first example the abbreviation is
three characters long, instead of the default of four.
# position of contrasts' bars (manual)
ggplot(mpg, aes(factor(cyl), hwy)) +
geom_boxplot(width = 0.33) +
stat_multcomp(p.adjust.method = "bonferroni",
adj.method.tag = 3,
size = 2.75) +
expand_limits(y = 0)
Here we use a negative value to use an abbreviation of the word “adjusted” to three characters.
# position of contrasts' bars (manual)
ggplot(mpg, aes(factor(cyl), hwy)) +
geom_boxplot(width = 0.33) +
stat_multcomp(p.adjust.method = "bonferroni",
adj.method.tag = -3,
size = 2.75) +
expand_limits(y = 0)
A character string passed as argument is used as is, here to set the tag in Spanish.
# position of contrasts' bars (manual)
ggplot(mpg, aes(factor(cyl), hwy)) +
geom_boxplot(width = 0.33) +
stat_multcomp(adj.method.tag = "ajustada",
size = 2.75) +
expand_limits(y = 0)
A numeric vector passed to label.y can be used to
manually set the location of each label along the y axis.
# position of contrasts' bars (manual)
ggplot(mpg, aes(factor(cyl), hwy)) +
geom_boxplot(width = 0.33) +
stat_multcomp(label.y = c(7, 4, 1),
contrasts = "Dunnet",
size = 2.75) +
expand_limits(y = 0)
ggplot(mpg, aes(factor(cyl), hwy)) +
geom_boxplot(width = 0.33) +
stat_multcomp(label.y =
seq(from = 15,
by = -3,
length.out = 6),
size = 2.5) +
expand_limits(y = 0)
We can pre-compute the numeric vector to achieve special positioning, in this case, next to each observation.
means <-
aggregate(mpg$hwy,
by = list(mpg$cyl),
FUN = mean,
na.rm = TRUE)[["x"]]
ggplot(mpg, aes(factor(cyl), hwy)) +
stat_summary(fun.data = mean_se) +
stat_multcomp(label.type = "letters",
label.y = c(18, means), # 18 is for critical P label
position = position_nudge(x = 0.1))
We can override the default use of geom_text() and also
remove the P critical label.
# Using other geometries
ggplot(mpg, aes(factor(cyl), hwy)) +
geom_boxplot(width = 0.33) +
stat_multcomp(label.type = "letters",
adj.method.tag = FALSE,
geom = "label")
With Dunnet contrasts, the use of bars can clutter a plot, and we can alternatively show the outcome for each level that has been compared to a control, the first level.
ggplot(mpg, aes(factor(cyl), hwy)) +
geom_boxplot(width = 0.33) +
stat_multcomp(aes(x = stage(start = factor(cyl),
after_stat = x.right.tip)),
geom = "text",
label.y = "bottom",
vstep = 0,
contrasts = "Dunnet")
ggplot(mpg, aes(factor(cyl), hwy)) +
geom_boxplot(width = 0.33) +
stat_multcomp(aes(x = stage(start = factor(cyl),
after_stat = x.right.tip),
label = after_stat(stars.label)),
geom = "text",
label.y = "bottom",
vstep = 0,
contrasts = "Dunnet")
The returned value includes numeric values in addition to character
strings mapped to the label aesthetic. The numeric values
can be used to encode the outcomes using additional or different
aesthetics than the default.
# use colour to show significance
ggplot(mpg, aes(factor(cyl), hwy)) +
geom_boxplot(width = 0.33) +
stat_multcomp(aes(colour = after_stat(p.value) < 0.01),
size = 2.75) +
scale_colour_manual(values = c("grey60", "black")) +
theme_bw()
# add arrow heads to segments and use fill to show significance
ggplot(mpg, aes(factor(cyl), hwy)) +
geom_boxplot(width = 0.33) +
stat_multcomp(aes(fill = after_stat(p.value) < 0.01),
size = 2.5,
arrow = grid::arrow(angle = 45,
length = unit(1, "mm"),
ends = "both")) +
scale_fill_manual(values = c("white", "lightblue"))
stat_fit_residuals
Sometimes we need to quickly plot residuals matching fits plotted
with stat_poly_line(), stat_quant_line(),
stat_ma_line() or ggplot2::stat_smooth()
(e.g., using grouping and facets). Function
stat_fit_residuals() makes this easy. In teaching it is
specially important to avoid distractions and plots residuals from
different types of models consistently.
stat_fit_residuals() can be used to plot the residuals
from models of y on x or x on y
fitted with function lm, MASS:rlm,
quantreg::rq (only median regression) or a user-supplied
model fitting function and arguments. In the data frame returned by the
statistic the response variable, y or x, is replaced
by the residuals from the fit and thus also by default mapped to the
aesthetic of the same name. The default geom is
"point".
formula <- y ~ poly(x, 3, raw = TRUE)
ggplot(my.data, aes(x, y, colour = group)) +
geom_hline(yintercept = 0, linetype = "dashed") +
stat_fit_residuals(formula = formula)
We can of course also map the weights returned in the model fit
object to ggplot2 aesthetics, here we use size.
formula <- y ~ poly(x, 3, raw = TRUE)
ggplot(my.data, aes(x, y, colour = group)) +
geom_hline(yintercept = 0, linetype = "dashed") +
stat_fit_residuals(formula = formula,
method = "rlm",
mapping = aes(size = sqrt(after_stat(weights))),
alpha = 2/3)
Weighted residuals are available, but in this case they do not differ
as we have not mapped any variable to the weight aesthetic
in the input to the statistic.
stat_fit_deviations
When teaching we may wish to highlight residuals in plots used in
slides and notes. Statistic stat_fit_deviations() makes it
easy to achieve this for the residuals from models of y on
x or x on y fitted with function
lm, MASS:rlm, quantreg::rq (only
median regression) or a user-supplied model fitting function and
arguments. The observed values are mapped to aesthetics x and
y, and the fitted values are mapped to aesthetics xend
and yend. As the default geom is "segment", each
deviation is displayed as a segment.
formula <- y ~ poly(x, 3, raw = TRUE)
ggplot(my.data, aes(x, y)) +
geom_smooth(method = "lm", formula = formula) +
stat_fit_deviations(formula = formula, colour = "red") +
geom_point()
The geometry used by default is ggplot2::geom_segment()
and additional aesthetics can be mapped or set to constant values. Here
we add arrowheads.
formula <- y ~ poly(x, 3, raw = TRUE)
ggplot(my.data, aes(x, y)) +
geom_smooth(method = "lm", formula = formula) +
geom_point() +
stat_fit_deviations(formula = formula, colour = "red",
arrow = arrow(length = unit(0.015, "npc"),
ends = "both"))
When weights are available, either supplied by the user, or computed
as part of the fit, they are returned in data. Having
weights available allows encoding them using colour. We here use a
robust regression fit with MASS::rlm().
my.data.outlier <- my.data
my.data.outlier[6, "y"] <- my.data.outlier[6, "y"] * 5
ggplot(my.data.outlier, aes(x, y)) +
stat_smooth(method = MASS::rlm, formula = formula) +
stat_fit_deviations(formula = formula, method = "rlm",
mapping = aes(colour = after_stat(weights)),
show.legend = TRUE) +
scale_color_gradient(low = "red", high = "blue", limits = c(0, 1)) +
geom_point()
stat_fit_glance
Package ‘broom’ provides consistently formatted output from different
model fitting functions. These made it possible to write a
model-annotation statistic that is very flexible but that requires
additional input from the user to generate the character strings to be
mapped to the label aesthetic.
As we have above given some simple examples, we here exemplify this statistic in a plot with grouping, and assemble a label for the P-value using a string parsed into a expression. We also change the default position of the labels.
# formula <- y ~ poly(x, 3, raw = TRUE)
# broom::augment does not handle poly() correctly!
formula <- y ~ x + I(x^2) + I(x^3)
ggplot(my.data, aes(x, y, colour = group)) +
geom_point() +
geom_smooth(method = "lm", formula = formula) +
stat_fit_glance(method = "lm",
method.args = list(formula = formula),
label.x = "right",
label.y = "bottom",
aes(label = sprintf("italic(P)*\"-value = \"*%.3g",
after_stat(p.value))),
parse = TRUE)
It is also possible to fit a non-linear model with
method = "nls", and any other model for which a
broom::glance() method exists. Do consult the documentation
for package ‘broom’. Here we fit the Michaelis-Menten equation to
reaction rate versus concentration data.
micmen.formula <- y ~ SSmicmen(x, Vm, K)
ggplot(Puromycin, aes(conc, rate, colour = state)) +
geom_point() +
geom_smooth(method = "nls",
formula = micmen.formula,
se = FALSE) +
stat_fit_glance(method = "nls",
method.args = list(formula = micmen.formula),
aes(label = paste("AIC = ", signif(after_stat(AIC), digits = 3),
", BIC = ", signif(after_stat(BIC), digits = 3),
sep = "")),
label.x = "centre", label.y = "bottom")
stat_fit_tb
This ggplot statistic makes it possible to add summary or ANOVA
tables for any fitted model for which broom::tidy() is
implemented. The output from broom::tidy() is embedded as a
single list value within the returned data, as an object of
class tibble::tibble.
This statistic ignores grouping based on aesthetics,
i.e., uses a panel function to fit the model. Fitting the model
by panel allows fitting models when x or y is
a factor (as in such cases ggplot splits the
data into groups, one for each level of the factor, which is needed for
example for stat_summary() to work as expected). By
default, the "table" geometry is used. The use of
ggpp::geom_table() is described in the User Guide of
package ‘ggpp’. Table themes and mapped aesthetics are supported.
The default output of stat_fit_tb() is the default
output from tidy(fm) where fm is the fitted
model.
formula <- y ~ x + I(x^2) + I(x^3)
ggplot(my.data, aes(x, y)) +
geom_point() +
geom_smooth(method = "lm", formula = formula) +
stat_fit_tb(method = "lm",
method.args = list(formula = formula),
tb.vars = c(Parameter = "term",
Estimate = "estimate",
"s.e." = "std.error",
"italic(t)" = "statistic",
"italic(P)" = "p.value"),
label.y = "top", label.x = "left",
parse = TRUE)
When tb.type = "fit.anova" the output returned is that
from tidy(anova(fm)) where fm is the fitted
model. Here we also show how to replace names of columns and terms, and
exclude one column, in this case, the mean squares.
formula <- y ~ x + I(x^2) + I(x^3)
ggplot(my.data, aes(x, y)) +
geom_point() +
geom_smooth(method = "lm", formula = formula) +
stat_fit_tb(method = "lm",
method.args = list(formula = formula),
tb.type = "fit.anova",
tb.vars = c(Effect = "term",
df = "df",
"italic(F)" = "statistic",
"italic(P)" = "p.value"),
tb.params = c(x = 1, "x^2" = 2, "x^3" = 3, Resid = 4),
label.y = "top", label.x = "left",
parse = TRUE)
When tb.type = "fit.coefs" the output returned is that
of tidy(fm) after selecting the term and
estimate columns.
formula <- y ~ x + I(x^2) + I(x^3)
ggplot(my.data, aes(x, y)) +
geom_point() +
geom_smooth(method = "lm", formula = formula) +
stat_fit_tb(method = "lm",
method.args = list(formula = formula),
tb.type = "fit.coefs", parse = TRUE,
label.y = "center", label.x = "left")
Faceting works as expected, but grouping is ignored as mentioned
above. In this case, the colour aesthetic is not applied to the text of
the tables. Furthermore, if label.x.npc or
label.y.npc are passed numeric vectors of length > 1,
the corresponding values are obeyed by the different panels.
micmen.formula <- y ~ SSmicmen(x, Vm, K)
ggplot(Puromycin, aes(conc, rate, colour = state)) +
facet_wrap(~state) +
geom_point() +
geom_smooth(method = "nls",
formula = micmen.formula,
se = FALSE) +
stat_fit_tb(method = "nls",
method.args = list(formula = micmen.formula),
tb.type = "fit.coefs",
label.x = 0.9,
label.y = c(0.75, 0.2)) +
theme(legend.position = "none") +
labs(x = "C", y = "V")
The data in the example below are split by ggplot into six groups
based on the levels of the feed factor. However, as
stat_fit_tb() ignores groupings, we can still fit a linear
model to all the data in the panel.
ggplot(chickwts, aes(factor(feed), weight)) +
stat_summary(fun.data = "mean_se") +
stat_fit_tb(tb.type = "fit.anova",
label.x = "center",
label.y = "bottom") +
expand_limits(y = 0)
We can flip the system of coordinates, if desired.
ggplot(chickwts, aes(factor(feed), weight)) +
stat_summary(fun.data = "mean_se") +
stat_fit_tb(tb.type = "fit.anova", label.x = "left", size = 3) +
scale_x_discrete(expand = expansion(mult = c(0.2, 0.5))) +
coord_flip()
It is also possible to rotate the table using angle.
Here we also show how to replace the column headers with strings to be
parsed into R expressions.
ggplot(chickwts, aes(factor(feed), weight)) +
stat_summary(fun.data = "mean_se") +
stat_fit_tb(tb.type = "fit.anova",
angle = 90, size = 3,
label.x = "right", label.y = "center",
hjust = 0.5, vjust = 0,
tb.vars = c(Effect = "term",
"df",
"M.S." = "meansq",
"italic(F)" = "statistic",
"italic(P)" = "p.value"),
parse = TRUE) +
scale_x_discrete(expand = expansion(mult = c(0.1, 0.35))) +
expand_limits(y = 0)
stat_fit_tidy
This stat makes it possible to add the equation for any fitted model
for which broom::tidy() is implemented. Alternatively,
individual values such as estimates for the fitted parameters, standard
errors, or P-values can be added to a plot. However, the user
has to explicitly construct the labels within
ggplot2::aes(). This statistic respects grouping based on
aesthetics, and reshapes the output of broom::tidy() so
that the values for a given group are in a single row in the returned
data.
As first example we fit a non-linear model, the Michaelis-Menten
equation of reaction kinetics, using stats::nls(). We use
the self-starting function stats::SSmicmen() available in
R.
micmen.formula <- y ~ SSmicmen(x, Vm, K)
ggplot(Puromycin, aes(conc, rate, colour = state)) +
geom_point() +
geom_smooth(method = "nls",
formula = micmen.formula,
se = FALSE) +
stat_fit_tidy(method = "nls",
method.args = list(formula = micmen.formula),
label.x = "right",
label.y = "bottom",
aes(label = paste("V[m]~`=`~", signif(after_stat(Vm_estimate), digits = 3),
"%+-%", signif(after_stat(Vm_se), digits = 2),
"~~~~K~`=`~", signif(after_stat(K_estimate), digits = 3),
"%+-%", signif(after_stat(K_se), digits = 2),
sep = "")),
parse = TRUE)
Using paste we can build a string that can be parsed into an R expression, in this case for a non-linear equation.
micmen.formula <- y ~ SSmicmen(x, Vm, K)
ggplot(Puromycin, aes(conc, rate, colour = state)) +
geom_point() +
geom_smooth(method = "nls",
formula = micmen.formula,
se = FALSE) +
stat_fit_tidy(method = "nls",
method.args = list(formula = micmen.formula),
size = 3,
label.x = "center",
label.y = "bottom",
vstep = 0.12,
aes(label = paste("V~`=`~frac(", signif(after_stat(Vm_estimate), digits = 2), "~C,",
signif(after_stat(K_estimate), digits = 2), "+C)",
sep = "")),
parse = TRUE) +
labs(x = "C", y = "V")
What if we would need a more specific statistic, similar to
stat_poly_eq()? We can use stat_fit_tidy() as
the basis for its definition.
stat_micmen_eq <- function(vstep = 0.12,
size = 3,
...) {
stat_fit_tidy(method = "nls",
method.args = list(formula = micmen.formula),
aes(label = paste("V~`=`~frac(", signif(after_stat(Vm_estimate), digits = 2), "~C,",
signif(after_stat(K_estimate), digits = 2), "+C)",
sep = "")),
parse = TRUE,
vstep = vstep,
size = size,
...)
}The code for the figure is now simpler, and still produces the same figure (not shown).
micmen.formula <- y ~ SSmicmen(x, Vm, K)
ggplot(Puromycin, aes(conc, rate, colour = state)) +
geom_point() +
geom_smooth(method = "nls",
formula = micmen.formula,
se = FALSE) +
stat_micmen_eq(label.x = "center",
label.y = "bottom") +
labs(x = "C", y = "V")
- As a second example we show a quantile regression fit using function
quantreg::rq()from package ‘quantreg’.
my_formula <- y ~ x
ggplot(mpg, aes(displ, 1 / hwy)) +
geom_point() +
geom_quantile(quantiles = 0.5, formula = my_formula) +
stat_fit_tidy(method = "rq",
method.args = list(formula = y ~ x, tau = 0.5),
tidy.args = list(se.type = "nid"),
mapping = aes(label = sprintf('y~"="~%.3g+%.3g~x*", with "*italic(P)~"="~%.3f',
after_stat(Intercept_estimate),
after_stat(x_estimate),
after_stat(x_p.value))),
parse = TRUE)
We can define a stat_rq_eq() if we need to add similar
equations to several plots. In this example we retain the ability of the
user to override most of the default default arguments.
stat_rq_eqn <-
function(formula = y ~ x,
tau = 0.5,
method = "br",
mapping = aes(label = sprintf('y~"="~%.3g+%.3g~x*", with "*italic(P)~"="~%.3f',
after_stat(Intercept_estimate),
after_stat(x_estimate),
after_stat(x_p.value))),
parse = TRUE,
...) {
method.args <- list(formula = formula, tau = tau, method = method)
stat_fit_tidy(method = "rq",
method.args = method.args,
tidy.args = list(se.type = "nid"),
mapping = mapping,
parse = parse,
...)
}And the code of the figure now as simple as. Figure not shown, as is identical to the one above.
ggplot(mpg, aes(displ, 1 / hwy)) +
geom_point() +
geom_quantile(quantiles = 0.5, formula = my_formula) +
stat_rq_eqn(tau = 0.5, formula = my_formula)
stat_fit_augment
Use ggplot2::stat_smooth, stat_poly_line(),
stat_ma_line(), stat_quant_line(),
stat_deviations() or stat_residuals() instead
of stat_fit_augment if possible.
When statistics specific to the type of model fitted are available,
their use is in general simpler that the use of
stat_fit_augment(). On the other hand,
stat_fit_augment() can handle any fitted model that is
supported by package ‘broom’ or its extensions. All these statistics
support grouping and facets.
# formula <- y ~ poly(x, 3, raw = TRUE)
# broom::augment does not handle poly correctly!
formula <- y ~ x + I(x^2) + I(x^3)
ggplot(my.data, aes(x, y)) +
geom_point() +
stat_fit_augment(method = "lm",
method.args = list(formula = formula))
formula <- y ~ x + I(x^2) + I(x^3)
ggplot(my.data, aes(x, y, colour = group)) +
geom_point() +
stat_fit_augment(method = "lm",
method.args = list(formula = formula))
We can override the variable returned as y to be any of
the variables in the data frame returned by
broom::augment() while still preserving the original
y values.
formula <- y ~ x + I(x^2) + I(x^3)
ggplot(my.data, aes(x, y)) +
stat_fit_augment(method = "lm",
method.args = list(formula = formula),
geom = "point",
y.out = ".resid")
formula <- y ~ x + I(x^2) + I(x^3)
ggplot(my.data, aes(x, y, colour = group)) +
stat_fit_augment(method = "lm",
method.args = list(formula = formula),
geom = "point",
y.out = ".std.resid")
We can use any model fitting method for which
broom::augment() is implemented.
args <- list(formula = y ~ k * e ^ x,
start = list(k = 1, e = 2))
ggplot(mtcars, aes(wt, mpg)) +
geom_point() +
stat_fit_augment(method = "nls",
method.args = args)## Warning in max(ids, na.rm = TRUE): no non-missing arguments to max; returning
## -Inf
args <- list(formula = y ~ k * e ^ x,
start = list(k = 1, e = 2))
ggplot(mtcars, aes(wt, mpg)) +
stat_fit_augment(method = "nls",
method.args = args,
geom = "point",
y.out = ".resid")
Note: The tidiers for mixed models have moved to package ‘broom.mixed’!
args <- list(model = y ~ SSlogis(x, Asym, xmid, scal),
fixed = Asym + xmid + scal ~1,
random = Asym ~1 | group,
start = c(Asym = 200, xmid = 725, scal = 350))
ggplot(Orange, aes(age, circumference, colour = Tree)) +
geom_point() +
stat_fit_augment(method = "nlme",
method.args = args,
augment.args = list(data = quote(data)))## Warning in max(ids, na.rm = TRUE): no non-missing arguments to max; returning
## -Inf
## Warning in max(ids, na.rm = TRUE): no non-missing arguments to max; returning
## -Inf
## Warning in max(ids, na.rm = TRUE): no non-missing arguments to max; returning
## -Inf
## Warning in max(ids, na.rm = TRUE): no non-missing arguments to max; returning
## -Inf
## Warning in max(ids, na.rm = TRUE): no non-missing arguments to max; returning
## -Inf
How to find out what variables are computed
When using stat_fit_glance(),
stat_fit_tidy(), stat_fit_augment() and
stat_fit_tb() the documentation cannot describe the
variables present in the returned data because they call
methods using their generic interface and the exact especialization used
depends on the argument passed to method, which can be even one that I
have not been aware of and never tested. Thanks to package ‘gginnards’
and its gginnards::geom_debug() we can find this out with a
temporary change to the plot code.
gginnards::geom_debug() uses by default
head() to echo to the R console the data it receives as
input. It ignores the aesthetic mappings so it can be used with any
statistics or directly as a layer function. However, unrecognised
aesthetics can trigger warnings during plot rendering. These warnings
can be ignored in most cases.
# formula <- y ~ poly(x, 3, raw = TRUE)
# broom::augment does not handle poly() correctly!
formula <- y ~ x + I(x^2) + I(x^3)
ggplot(my.data, aes(x, y, colour = group)) +
geom_point() +
geom_smooth(method = "lm", formula = formula) +
stat_fit_glance(geom = "debug",
method = "lm",
method.args = list(formula = formula),
label.x = "right",
label.y = "bottom",
aes(label = sprintf("italic(P)*\"-value = \"*%.3g",
after_stat(p.value))),
parse = TRUE)## Warning in stat_fit_glance(geom = "debug", method = "lm", method.args =
## list(formula = formula), : Ignoring unknown parameters: `parse`## [1] "PANEL 1; group(s) 1, 2; 'draw_function()' input 'data' (head):"
## colour npcx npcy label r.squared adj.r.squared
## 1 #F8766D NA NA italic(P)*"-value = "*1.24e-32 0.9619032 0.9594187
## 2 #00BFC4 NA NA italic(P)*"-value = "*1.73e-33 0.9650270 0.9627461
## sigma statistic p.value df logLik AIC BIC deviance
## 1 0.05391446 387.1505 1.237801e-32 3 77.15544 -144.3109 -134.7508 0.1337114
## 2 0.05521918 423.0996 1.732868e-33 3 75.95986 -141.9197 -132.3596 0.1402613
## df.residual nobs fm.class fm.method fm.formula
## 1 46 50 lm lm y ~ x + I(x^2) + I(x^3)
## 2 46 50 lm lm y ~ x + I(x^2) + I(x^3)
## fm.formula.chr x y PANEL group
## 1 y ~ x + I(x^2) + I(x^3) 95.05 -0.03289940 1 1
## 2 y ~ x + I(x^2) + I(x^3) 95.05 0.04864529 1 2
In the case of stat_fit_tb() the computed variables
returned include a list column containing embedded data frames. In this
case, function str() is more informative than
head(), so we can pass it as argument overriding the
default.
formula <- y ~ x + I(x^2) + I(x^3)
ggplot(my.data, aes(x, y)) +
geom_point() +
geom_smooth(method = "lm", formula = formula) +
stat_fit_tb(geom = "debug",
summary.fun = str,
method = "lm",
method.args = list(formula = formula),
tb.vars = c(Parameter = "term",
Estimate = "estimate",
"s.e." = "std.error",
"italic(t)" = "statistic",
"italic(P)" = "p.value"),
label.y = "top", label.x = "left",
parse = TRUE)## Warning in stat_fit_tb(geom = "debug", summary.fun = str, method = "lm", : Ignoring unknown parameters: `table.theme`, `table.rownames`, `table.colnames`,
## `table.hjust`, `parse`, and `summary.fun`## [1] "PANEL 1; group(s) NULL; 'draw_function()' input 'data' (head):"
## label
## 1 (Intercept), x, I(x^2), I(x^3), -0.0045, 0.00109, -2.14e-05, 1.06e-06, 0.0227, 0.00194, 4.44e-05, 2.89e-07, -0.198, 0.563, -0.482, 3.65, 0.843, 0.575, 0.631, < 0.001
## PANEL x y
## 1 1 1 1
## fm.tb
## 1 (Intercept), x, I(x^2), I(x^3), -0.0045, 0.00109, -2.14e-05, 1.06e-06, 0.0227, 0.00194, 4.44e-05, 2.89e-07, -0.198, 0.563, -0.482, 3.65, 0.843, 0.575, 0.631, < 0.001
## fm.tb.type fm.class fm.method fm.formula
## 1 fit.summary lm lm y ~ x + I(x^2) + I(x^3)
## fm.formula.chr npcx npcy
## 1 y ~ x + I(x^2) + I(x^3) NA NA
gginnards::geom_debug() can be used with ‘ggplot2’ and
its extensions. More examples are given in the documentation of
package ‘gginnards’.
Scales
Volcano and quadrant plots are scatter plots with some peculiarities. Creating these plots from scratch using ‘ggplot2’ can be time consuming, but allows flexibility in design. Rather than providing a ‘canned’ function to produce volcano plots, package ‘ggpmisc’ provides several building blocks that facilitate the production of volcano and quadrant plots. These are wrappers on scales from packages ‘scales’ and ‘ggplot2’ with suitable defaults plus helper functions to create factors from numeric outcomes.
scale_color_outcome, scale_fill_outcome
Manual scales for colour and fill aesthetics with defaults suitable for the three way outcomes from statistical tests.
scale_x_FDR, scale_y_FDR, scale_x_logFC, scale_y_logFC, scale_x_Pvalue, scale_y_Pvalue
Scales for x or y aesthetics mapped to P-values, FDR (false discovery rate) or log FC (logarithm of fold-change) as used in volcano and quadrant plots of transcriptomics and metabolomics data.
symmetric_limits
A simple function to expand scale limits to be symmetric around zero. Can be passed as argument to parameter limits of continuous scales from packages ‘ggpmisc’, ‘ggplot2’ or ‘scales’ (and extensions).
Volcano-plot examples
Volcano plots are frequently used for transcriptomics and metabolomics. They are used to show P-values or FDR (false discovery rate) as a function of effect size, which can be either an increase or a decrease. Effect sizes are expressed as fold-changes compared to a control or reference condition. Colours are frequently used to highlight significant responses. Counts of significant increases and decreases are frequently also added.
Outcomes encoded as -1, 0 or 1, as seen in the tibble below need to
be converted into factors with suitable labels for levels. This can be
easily achieved with function outcome2factor().
## tag gene outcome logFC PValue genotype
## 1 AT1G01040 ASU1 0 -0.15284466 0.35266997 Ler
## 2 AT1G01290 ASG4 0 -0.30057068 0.05471732 Ler
## 3 AT1G01560 ATSBT1.1 0 -0.57783350 0.06681310 Ler
## 4 AT1G01790 AtSAM1 0 -0.04729662 0.74054263 Ler
## 5 AT1G02130 AtTRM82 0 -0.14279891 0.29597519 Ler
## 6 AT1G02560 PRP39 0 0.23320752 0.07487043 LerMost frequently fold-change data is available log-transformed, using either 2 or 10 as base. In general it is more informative to use tick labels expressed as un-transformed fold-change.
By default scale_x_logFC() and
scale_y_logFC() expect the logFC data log2-transformed, but
this can be overridden. The default use of untransformed fold-change for
tick labels can also be overridden. Scale scale_x_logFC()
in addition by default expands the scale limits to make them symmetric
around zero. If %unit is included in the name character
string, suitable units are appended as shown in the example below.
Scales scale_y_Pvalue() and
scale_x_Pvalue() have suitable defaults for name and
labels, while scale_colour_outcome() provides suitable
defaults for the colours mapped to the outcomes. To change the labels
and title of the key or guide pass suitable
arguments to parameters name and labels of
these scales. These x and y scales by default squish off-limits
(out-of-bounds) observations towards the limits.
ggplot(volcano_example.df,
aes(logFC, PValue, colour = outcome2factor(outcome))) +
geom_point() +
scale_x_logFC(name = "Transcript abundance%unit") +
scale_y_Pvalue() +
scale_colour_outcome() +
stat_quadrant_counts(data = function(x) {subset(x, outcome != 0)})
By default outcome2factor() creates a factor with three
levels as in the example above, but this default can be overridden as
shown below.
ggplot(volcano_example.df,
aes(logFC, PValue, colour = outcome2factor(outcome, n.levels = 2))) +
geom_point() +
scale_x_logFC(name = "Transcript abundance%unit") +
scale_y_Pvalue() +
scale_colour_outcome(values = "outcome:de") +
stat_quadrant_counts(data = function(x) {subset(x, outcome != 0)})
Quadrant-plot examples
Quadrant plots are scatter plots with comparable variables on both axes and usually include the four quadrants. When used for transcriptomics and metabolomics, they are used to compare responses expressed as fold-change to two different conditions or treatments. They are useful when many responses are measured as in transcriptomics (many different genes) or metabolomics (many different metabolites).
A single panel quadrant plot is as easy to produce as a volcano plot
using scales scale_x_logFC() and
scale_y_logFC(). The data includes two different outcomes
and two different log fold-change variables. See the previous section on
volcano plots for details. In this example we use as shape a filled
circle and map one of the outcomes to colour and the other to fill,
using the two matched scales scale_colour_outcome() and
scale_fill_outcome().
## tag gene outcome.x outcome.y logFC.x logFC.y genotype
## 1 AT5G11060 TIC56 0 0 -0.17685517 -0.32956762 Ler
## 2 AT3G01280 ATWRKY48 0 0 -0.06471884 0.07771315 Ler
## 3 AT5G06320 ANY1 0 0 -0.35200684 -0.04331339 Ler
## 4 AT1G05850 AP1M1 0 0 -0.40284744 -0.04505435 Ler
## 5 AT2G22300 HSA32 0 0 -0.34482142 -0.11185095 Ler
## 6 AT2G16070 UBQ11 0 0 -0.22328946 -0.23210780 LerIn this plot we do not include those genes whose change in transcript abundance is uncertain under both x and y conditions.
ggplot(subset(quadrant_example.df,
xy_outcomes2factor(outcome.x, outcome.y) != "none"),
aes(logFC.x, logFC.y,
colour = outcome2factor(outcome.x),
fill = outcome2factor(outcome.y))) +
geom_quadrant_lines(linetype = "dotted") +
stat_quadrant_counts(size = 3, colour = "white") +
geom_point(shape = "circle filled") +
scale_x_logFC(name = "Transcript abundance for x%unit") +
scale_y_logFC(name = "Transcript abundance for y%unit") +
scale_colour_outcome() +
scale_fill_outcome() +
theme_dark()
To plot in separate panels those observations that are significant along both x and y axes, x axis, y axis, or none, with quadrants merged takes more effort. We first define two helper functions to add counts and quadrant lines to each of the four panels.
all_quadrant_counts <- function(...) {
list(
stat_quadrant_counts(data = . %>% filter(outcome.xy.fct == "xy"), ...),
stat_quadrant_counts(data = . %>% filter(outcome.xy.fct == "x"), pool.along = "y", ...),
stat_quadrant_counts(data = . %>% filter(outcome.xy.fct == "y"), pool.along = "x", ...),
stat_quadrant_counts(data = . %>% filter(outcome.xy.fct == "none"), quadrants = 0L, ...)
)
}all_quadrant_lines <- function(...) {
list(
geom_hline(data = data.frame(outcome.xy.fct = factor(c("xy", "x", "y", "none"),
levels = c("xy", "x", "y", "none")),
yintercept = c(0, NA, 0, NA)),
aes(yintercept = yintercept),
na.rm = TRUE,
...),
geom_vline(data = data.frame(outcome.xy.fct = factor(c("xy", "x", "y", "none"),
levels = c("xy", "x", "y", "none")),
xintercept = c(0, 0, NA, NA)),
aes(xintercept = xintercept),
na.rm = TRUE,
...)
)
}And use these functions to build the final plot, in this case including all genes.
quadrant_example.df %>%
mutate(.,
outcome.x.fct = outcome2factor(outcome.x),
outcome.y.fct = outcome2factor(outcome.y),
outcome.xy.fct = xy_outcomes2factor(outcome.x, outcome.y)) %>%
ggplot(., aes(logFC.x, logFC.y, colour = outcome.x.fct, fill = outcome.y.fct)) +
geom_point(shape = 21) +
all_quadrant_lines(linetype = "dotted") +
all_quadrant_counts(size = 3, colour = "white") +
scale_x_logFC(name = "Transcript abundance for x%unit") +
scale_y_logFC(name = "Transcript abundance for y%unit") +
scale_colour_outcome() +
scale_fill_outcome() +
facet_wrap(~outcome.xy.fct) +
theme_dark()