Type: |
Package |
Version: |
0.0.7 |
Title: |
Quantile-Quantile Plot Extensions for 'ggplot2' |
Description: |
Extensions of 'ggplot2' Q-Q plot functionalities. |
URL: |
https://github.com/aloy/qqplotr |
BugReports: |
https://github.com/aloy/qqplotr/issues |
License: |
GPL-3 | file LICENSE |
Encoding: |
UTF-8 |
LazyData: |
true |
RoxygenNote: |
7.3.2 |
Collate: |
'data.R' 'geom_qq_band.R' 'qqplotr.R' 'runShinyExample.R'
'stat_pp_band.R' 'stat_pp_line.R' 'stat_pp_point.R'
'stat_qq_line.R' 'stat_qq_band.R' 'stat_qq_point.R' |
VignetteBuilder: |
knitr |
Depends: |
R (≥ 3.1), ggplot2 (≥ 2.2) |
Imports: |
dplyr, robustbase, MASS, opdisDownsampling, qqconf (≥ 1.3.1) |
Suggests: |
shiny, devtools, lattice, shinyBS, knitr, rmarkdown |
NeedsCompilation: |
no |
Packaged: |
2025-09-05 01:14:45 UTC; aloy |
Author: |
Alexandre Almeida [aut],
Adam Loy [aut, cre],
Heike Hofmann [aut] |
Maintainer: |
Adam Loy <loyad01@gmail.com> |
Repository: |
CRAN |
Date/Publication: |
2025-09-05 17:00:02 UTC |
Q-Q and P-P plot extensions for 'ggplot2'
Description
This package extends some ggplot2
functionalities by permitting the
drawing of both quantile-quantile (Q-Q) and probability-probability (P-P)
points, lines, and confidence bands. The functions of this package also allow
the detrend adjustment, proposed by Thode (2002), which helps reduce visual
bias when assessing those plots.
Details
The functions of this package, presented as ggplot2
Stats, are divided
into two groups: Q-Q and P-P related.
Each of the groups is composed of three Stats: point
, line
, and
band
. Those Stats, while independent, complement each other when
plotted together.
Author(s)
Maintainer: Adam Loy loyad01@gmail.com
Authors:
See Also
Useful links:
GeomQqBand
Description
GeomQqBand
Format
An object of class GeomQqBand
(inherits from Geom
, ggproto
, gg
) of length 6.
StatPpBand
Description
StatPpBand
Format
An object of class StatPpBand
(inherits from Stat
, ggproto
, gg
) of length 5.
StatPpLine
Description
StatPpLine
Format
An object of class StatPpLine
(inherits from Stat
, ggproto
, gg
) of length 5.
StatPpPoint
Description
StatPpPoint
Format
An object of class StatPpPoint
(inherits from Stat
, ggproto
, gg
) of length 5.
StatQqBand
Description
StatQqBand
Format
An object of class StatQqBand
(inherits from StatQqLine
, Stat
, ggproto
, gg
) of length 5.
StatQqLine
Description
StatQqLine
Format
An object of class StatQqLine
(inherits from Stat
, ggproto
, gg
) of length 5.
StatQqPoint
Description
StatQqPoint
Format
An object of class StatQqPoint
(inherits from Stat
, ggproto
, gg
) of length 5.
Quantile-quantile confidence bands
Description
Draws quantile-quantile confidence bands, with an additional detrend option.
Usage
geom_qq_band(
mapping = NULL,
data = NULL,
stat = "qq_band",
position = "identity",
na.rm = TRUE,
show.legend = NA,
inherit.aes = TRUE,
distribution = "norm",
dparams = list(),
detrend = FALSE,
identity = FALSE,
qtype = 7,
qprobs = c(0.25, 0.75),
bandType = "pointwise",
B = 1000,
conf = 0.95,
mu = NULL,
sigma = NULL,
...
)
stat_qq_band(
mapping = NULL,
data = NULL,
geom = "qq_band",
position = "identity",
na.rm = TRUE,
show.legend = NA,
inherit.aes = TRUE,
distribution = "norm",
dparams = list(),
detrend = FALSE,
identity = FALSE,
qtype = 7,
qprobs = c(0.25, 0.75),
bandType = "pointwise",
B = 1000,
conf = 0.95,
mu = NULL,
sigma = NULL,
...
)
Arguments
mapping |
Set of aesthetic mappings created by aes() . If specified and
inherit.aes = TRUE (the default), it is combined with the default mapping
at the top level of the plot. You must supply mapping if there is no plot
mapping.
|
data |
The data to be displayed in this layer. There are three
options:
If NULL , the default, the data is inherited from the plot
data as specified in the call to ggplot() .
A data.frame , or other object, will override the plot
data. All objects will be fortified to produce a data frame. See
fortify() for which variables will be created.
A function will be called with a single argument,
the plot data. The return value must be a data.frame , and
will be used as the layer data. A function can be created
from a formula (e.g. ~ head(.x, 10) ).
|
stat |
statistic to use to calculate confidence bands. Should be
'qq_band'.
|
position |
A position adjustment to use on the data for this layer. This
can be used in various ways, including to prevent overplotting and
improving the display. The position argument accepts the following:
The result of calling a position function, such as position_jitter() .
This method allows for passing extra arguments to the position.
A string naming the position adjustment. To give the position as a
string, strip the function name of the position_ prefix. For example,
to use position_jitter() , give the position as "jitter" .
For more information and other ways to specify the position, see the
layer position documentation.
|
na.rm |
If FALSE , the default, missing values are removed with
a warning. If TRUE , missing values are silently removed.
|
show.legend |
logical. Should this layer be included in the legends?
NA , the default, includes if any aesthetics are mapped.
FALSE never includes, and TRUE always includes.
It can also be a named logical vector to finely select the aesthetics to
display. To include legend keys for all levels, even
when no data exists, use TRUE . If NA , all levels are shown in legend,
but unobserved levels are omitted.
|
inherit.aes |
If FALSE, overrides the default aesthetics, rather than
combining with them. This is most useful for helper functions that define
both data and aesthetics and shouldn't inherit behaviour from the default
plot specification
|
distribution |
Character. Theoretical probability distribution function
to use. Do not provide the full distribution function name (e.g.,
"dnorm" ). Instead, just provide its shortened name (e.g.,
"norm" ). If you wish to provide a custom distribution, you may do so
by first creating the density, quantile, and random functions following the
standard nomenclature from the stats package (i.e., for
"custom" , create the dcustom , pcustom ,
qcustom , and rcustom functions).
|
dparams |
List of additional parameters passed on to the previously
chosen distribution function. If an empty list is provided (default)
then the distributional parameters are estimated via MLE. MLE for custom
distributions is currently not supported, so you must provide the
appropriate dparams in that case.
|
detrend |
Logical. Should the plot objects be detrended? If TRUE ,
the objects will be detrended according to the reference Q-Q line. This
procedure was described by Thode (2002), and may help reducing visual bias
caused by the orthogonal distances from Q-Q points to the reference line.
|
identity |
Logical. Should an identity line be used as the reference
line used to construct the confidence bands? If TRUE , the identity
line is used. If FALSE (default), the commonly-used Q-Q line that
intercepts two data quantiles specified in qprobs is used. Please
notice that the chosen reference line will also be used for the detrending
procedure, if detrend = TRUE .
|
qtype |
Integer between 1 and 9. Type of the quantile algorithm to be
used by the quantile function to construct the Q-Q
line.
|
qprobs |
Numeric vector of length two. Represents the quantiles used by
the quantile function to construct the Q-Q line.
|
bandType |
Character. Either "pointwise" , "boot" , "ks" or
"ts" , or "ell" . "pointwise" constructs pointwise confidence bands based
on Normal confidence intervals. "boot" creates pointwise confidence
bands based on a parametric bootstrap; parameters are estimated with MLEs.
"ks" constructs simultaneous confidence bands based on the Kolmogorov-Smirnov
test. "ts" constructs tail-sensitive confidence bands, as
described by Aldor-Noiman et al. (2013) (also, see 'Note' for
limitations). Finally, "ell" constructs simultaenous bands using the
equal local levels test describe by Weine et al. (2021).
|
B |
Integer. If bandType = "boot" , then B is the number of
bootstrap replicates. If bandType = "ts" , then B is the
number of simulated samples.
|
conf |
Numerical. Confidence level of the bands.
|
mu |
Numerical. Only used if bandType = "ts" . Center
distributional parameter used to construct the simulated tail-sensitive
confidence bands. If either mu or sigma are NULL , then
those parameters are estimated using Qn and
s_Qn , respectively.
|
sigma |
Numerical. Only used if bandType = "ts" . Scale
distributional parameter used to construct the simulated tail-sensitive
confidence bands. If either mu or sigma are NULL , then
those parameters are estimated using robust estimates from the stats
package.
|
... |
Other arguments passed on to layer() 's params argument. These
arguments broadly fall into one of 4 categories below. Notably, further
arguments to the position argument, or aesthetics that are required
can not be passed through ... . Unknown arguments that are not part
of the 4 categories below are ignored.
Static aesthetics that are not mapped to a scale, but are at a fixed
value and apply to the layer as a whole. For example, colour = "red"
or linewidth = 3 . The geom's documentation has an Aesthetics
section that lists the available options. The 'required' aesthetics
cannot be passed on to the params . Please note that while passing
unmapped aesthetics as vectors is technically possible, the order and
required length is not guaranteed to be parallel to the input data.
When constructing a layer using
a stat_*() function, the ... argument can be used to pass on
parameters to the geom part of the layer. An example of this is
stat_density(geom = "area", outline.type = "both") . The geom's
documentation lists which parameters it can accept.
Inversely, when constructing a layer using a
geom_*() function, the ... argument can be used to pass on parameters
to the stat part of the layer. An example of this is
geom_area(stat = "density", adjust = 0.5) . The stat's documentation
lists which parameters it can accept.
The key_glyph argument of layer() may also be passed on through
... . This can be one of the functions described as
key glyphs, to change the display of the layer in the legend.
|
geom |
The geometric object to use to display the data for this layer.
When using a stat_*() function to construct a layer, the geom argument
can be used to override the default coupling between stats and geoms. The
geom argument accepts the following:
A Geom ggproto subclass, for example GeomPoint .
A string naming the geom. To give the geom as a string, strip the
function name of the geom_ prefix. For example, to use geom_point() ,
give the geom as "point" .
For more information and other ways to specify the geom, see the
layer geom documentation.
|
Note
Tail-sensitive confidence bands are only implemented for Normal Q-Q
plots. As a future update, we intend to generalize to other distributions.
Bootstrap bands are constructed based on a MLE parametric bootstrap.
Hence, it is not possible to construct such bands if the sample and
theoretical distributions present mismatching supports.
References
Examples
# generate random Normal data
set.seed(0)
smp <- data.frame(norm = rnorm(100))
# Normal Q-Q plot of Normal data
gg <- ggplot(data = smp, mapping = aes(sample = norm)) +
stat_qq_band() +
stat_qq_line() +
stat_qq_point()
gg + labs(x = "Theoretical Quantiles", y = "Sample Quantiles")
# Normal Q-Q plot of Normal data with equal local levels (ell) bands
bt <- "ell"
gg <- ggplot(data = smp, mapping = aes(sample = norm)) +
stat_qq_band(bandType = bt) +
stat_qq_line() +
stat_qq_point() +
labs(x = "Theoretical Quantiles", y = "Sample Quantiles")
gg
# Exponential Q-Q plot of mean ozone levels (airquality dataset)
di <- "exp"
dp <- list(rate = 1)
gg <- ggplot(data = airquality, mapping = aes(sample = Ozone)) +
stat_qq_band(distribution = di, dparams = dp) +
stat_qq_line(distribution = di, dparams = dp) +
stat_qq_point(distribution = di, dparams = dp) +
labs(x = "Theoretical Quantiles", y = "Sample Quantiles")
gg
# Detrended Exponential Q-Q plot of mean ozone levels
di <- "exp"
dp <- list(rate = 1)
de <- TRUE
gg <- ggplot(data = airquality, mapping = aes(sample = Ozone)) +
stat_qq_band(distribution = di, detrend = de) +
stat_qq_line(distribution = di, detrend = de) +
stat_qq_point(distribution = di, detrend = de) +
labs(x = "Theoretical Quantiles", y = "Sample Quantiles")
gg
## Not run:
# Normal Q-Q plot of Normal data with bootstrap confidence bands
bt <- "boot"
gg <- ggplot(data = smp, mapping = aes(sample = norm)) +
stat_qq_band(bandType = bt) +
stat_qq_line() +
stat_qq_point() +
labs(x = "Theoretical Quantiles", y = "Sample Quantiles")
gg
# Normal Q-Q plot of Normal data with tail-sensitive confidence bands
bt <- "ts"
gg <- ggplot(data = smp, mapping = aes(sample = norm)) +
stat_qq_band(bandType = bt) +
stat_qq_line() +
stat_qq_point() +
labs(x = "Theoretical Quantiles", y = "Sample Quantiles")
gg
## End(Not run)
2012 BRFSS sample for the state of Iowa
Description
2012 BRFSS sample for the state of Iowa
Usage
data(iowa)
Format
A data frame with 7166 observations on 3 variables:
- SEX
Gender
- WTKG3
Weight in kg
- HTIN4
Height in inch
Source
https://www.cdc.gov/brfss/annual_data/annual_2012.html
Men's Olympic Long Jump Qualifiers 2012
Description
Men's Olympic Long Jump Qualifiers 2012
Usage
data(longjump)
Format
A data frame with 42 observations on the following 4 variables:
- rank
Athlete's rank at the qualifying event
- name
Athlete's name
- country
Athlete's country of origin
- distance
Result in meters
Source
https://www.olympics.com/en/olympic-games/london-2012/results/athletics/long-jump-men
'qqplotr' Example Shiny App
Description
'qqplotr' Example Shiny App
Probability-probability confidence bands
Description
Draws probability-probability confidence bands.
Usage
stat_pp_band(
mapping = NULL,
data = NULL,
geom = "ribbon",
position = "identity",
na.rm = TRUE,
show.legend = NA,
inherit.aes = TRUE,
distribution = "norm",
dparams = list(),
bandType = "boot",
B = 1000,
conf = 0.95,
detrend = FALSE,
...
)
Arguments
mapping |
Set of aesthetic mappings created by aes() . If specified and
inherit.aes = TRUE (the default), it is combined with the default mapping
at the top level of the plot. You must supply mapping if there is no plot
mapping.
|
data |
The data to be displayed in this layer. There are three
options:
If NULL , the default, the data is inherited from the plot
data as specified in the call to ggplot() .
A data.frame , or other object, will override the plot
data. All objects will be fortified to produce a data frame. See
fortify() for which variables will be created.
A function will be called with a single argument,
the plot data. The return value must be a data.frame , and
will be used as the layer data. A function can be created
from a formula (e.g. ~ head(.x, 10) ).
|
geom |
The geometric object to use to display the data for this layer.
When using a stat_*() function to construct a layer, the geom argument
can be used to override the default coupling between stats and geoms. The
geom argument accepts the following:
A Geom ggproto subclass, for example GeomPoint .
A string naming the geom. To give the geom as a string, strip the
function name of the geom_ prefix. For example, to use geom_point() ,
give the geom as "point" .
For more information and other ways to specify the geom, see the
layer geom documentation.
|
position |
A position adjustment to use on the data for this layer. This
can be used in various ways, including to prevent overplotting and
improving the display. The position argument accepts the following:
The result of calling a position function, such as position_jitter() .
This method allows for passing extra arguments to the position.
A string naming the position adjustment. To give the position as a
string, strip the function name of the position_ prefix. For example,
to use position_jitter() , give the position as "jitter" .
For more information and other ways to specify the position, see the
layer position documentation.
|
na.rm |
If FALSE , the default, missing values are removed with
a warning. If TRUE , missing values are silently removed.
|
show.legend |
logical. Should this layer be included in the legends?
NA , the default, includes if any aesthetics are mapped.
FALSE never includes, and TRUE always includes.
It can also be a named logical vector to finely select the aesthetics to
display. To include legend keys for all levels, even
when no data exists, use TRUE . If NA , all levels are shown in legend,
but unobserved levels are omitted.
|
inherit.aes |
If FALSE, overrides the default aesthetics, rather than
combining with them. This is most useful for helper functions that define
both data and aesthetics and shouldn't inherit behaviour from the default
plot specification
|
distribution |
Character. Theoretical probability distribution function
to use. Do not provide the full distribution function name (e.g.,
"dnorm" ). Instead, just provide its shortened name (e.g.,
"norm" ). If you wish to provide a custom distribution, you may do so
by first creating the density, quantile, and random functions following the
standard nomenclature from the stats package (i.e., for
"custom" , create the dcustom , pcustom ,
qcustom , and rcustom functions).
|
dparams |
List of additional parameters passed on to the previously
chosen distribution function. If an empty list is provided (default)
then the distributional parameters are estimated via MLE. MLE for custom
distributions is currently not supported, so you must provide the
appropriate dparams in that case.
|
bandType |
Character. Only "boot" and "ell" are available for now. "boot"
creates pointwise confidence bands based on a bootstrap. "ell"
constructs simultaenous bands using the equal local levels test.
|
B |
Integer. If bandType = "boot" , then B is the number of
bootstrap replicates.
|
conf |
Numerical. Confidence level of the bands.
|
detrend |
Logical. Should the plot objects be detrended? If TRUE ,
the objects will be detrended according to the default identity P-P line.
This procedure was described by Thode (2002), and may help reducing visual
bias caused by the orthogonal distances from P-P points to the reference
line.
|
... |
Other arguments passed on to layer() 's params argument. These
arguments broadly fall into one of 4 categories below. Notably, further
arguments to the position argument, or aesthetics that are required
can not be passed through ... . Unknown arguments that are not part
of the 4 categories below are ignored.
Static aesthetics that are not mapped to a scale, but are at a fixed
value and apply to the layer as a whole. For example, colour = "red"
or linewidth = 3 . The geom's documentation has an Aesthetics
section that lists the available options. The 'required' aesthetics
cannot be passed on to the params . Please note that while passing
unmapped aesthetics as vectors is technically possible, the order and
required length is not guaranteed to be parallel to the input data.
When constructing a layer using
a stat_*() function, the ... argument can be used to pass on
parameters to the geom part of the layer. An example of this is
stat_density(geom = "area", outline.type = "both") . The geom's
documentation lists which parameters it can accept.
Inversely, when constructing a layer using a
geom_*() function, the ... argument can be used to pass on parameters
to the stat part of the layer. An example of this is
geom_area(stat = "density", adjust = 0.5) . The stat's documentation
lists which parameters it can accept.
The key_glyph argument of layer() may also be passed on through
... . This can be one of the functions described as
key glyphs, to change the display of the layer in the legend.
|
References
Examples
# generate random Normal data
set.seed(0)
smp <- data.frame(norm = rnorm(100), exp = rexp(100))
# Normal P-P plot of Normal data
gg <- ggplot(data = smp, mapping = aes(sample = norm)) +
stat_pp_band() +
stat_pp_line() +
stat_pp_point() +
labs(x = "Probability Points", y = "Cumulative Probability")
gg
# Shifted Normal P-P plot of Normal data
dp <- list(mean = 1.5)
gg <- ggplot(data = smp, mapping = aes(sample = norm)) +
stat_pp_band(dparams = dp, bandType = "ell") +
stat_pp_line() +
stat_pp_point(dparams = dp) +
labs(x = "Probability Points", y = "Cumulative Probability")
gg
# Exponential P-P plot of Exponential data
di <- "exp"
gg <- ggplot(data = smp, mapping = aes(sample = exp)) +
stat_pp_band(distribution = di, bandType = "ell") +
stat_pp_line() +
stat_pp_point(distribution = di) +
labs(x = "Probability Points", y = "Cumulative Probability")
gg
## Not run:
# Normal P-P plot of mean ozone levels (airquality dataset)
dp <- list(mean = 38, sd = 27)
gg <- ggplot(data = airquality, mapping = aes(sample = Ozone)) +
stat_pp_band(dparams = dp) +
stat_pp_line() +
stat_pp_point(dparams = dp) +
labs(x = "Probability Points", y = "Cumulative Probability")
gg
## End(Not run)
Probability-probability lines
Description
Draws a probability-probability line.
Usage
stat_pp_line(
mapping = NULL,
data = NULL,
geom = "path",
position = "identity",
na.rm = TRUE,
show.legend = NA,
inherit.aes = TRUE,
ab = c(0, 1),
detrend = FALSE,
...
)
Arguments
mapping |
Set of aesthetic mappings created by aes() . If specified and
inherit.aes = TRUE (the default), it is combined with the default mapping
at the top level of the plot. You must supply mapping if there is no plot
mapping.
|
data |
The data to be displayed in this layer. There are three
options:
If NULL , the default, the data is inherited from the plot
data as specified in the call to ggplot() .
A data.frame , or other object, will override the plot
data. All objects will be fortified to produce a data frame. See
fortify() for which variables will be created.
A function will be called with a single argument,
the plot data. The return value must be a data.frame , and
will be used as the layer data. A function can be created
from a formula (e.g. ~ head(.x, 10) ).
|
geom |
The geometric object to use to display the data for this layer.
When using a stat_*() function to construct a layer, the geom argument
can be used to override the default coupling between stats and geoms. The
geom argument accepts the following:
A Geom ggproto subclass, for example GeomPoint .
A string naming the geom. To give the geom as a string, strip the
function name of the geom_ prefix. For example, to use geom_point() ,
give the geom as "point" .
For more information and other ways to specify the geom, see the
layer geom documentation.
|
position |
A position adjustment to use on the data for this layer. This
can be used in various ways, including to prevent overplotting and
improving the display. The position argument accepts the following:
The result of calling a position function, such as position_jitter() .
This method allows for passing extra arguments to the position.
A string naming the position adjustment. To give the position as a
string, strip the function name of the position_ prefix. For example,
to use position_jitter() , give the position as "jitter" .
For more information and other ways to specify the position, see the
layer position documentation.
|
na.rm |
If FALSE , the default, missing values are removed with
a warning. If TRUE , missing values are silently removed.
|
show.legend |
logical. Should this layer be included in the legends?
NA , the default, includes if any aesthetics are mapped.
FALSE never includes, and TRUE always includes.
It can also be a named logical vector to finely select the aesthetics to
display. To include legend keys for all levels, even
when no data exists, use TRUE . If NA , all levels are shown in legend,
but unobserved levels are omitted.
|
inherit.aes |
If FALSE, overrides the default aesthetics, rather than
combining with them. This is most useful for helper functions that define
both data and aesthetics and shouldn't inherit behaviour from the default
plot specification
|
ab |
Numeric vector of length two. The intercept (a ) and slope
(b ) of the P-P line. Defaults to the identity line (a = 0, b =
1 ).
|
detrend |
Logical. Should the plot objects be detrended? If TRUE ,
the objects will be detrended according to the default identity P-P line.
This procedure was described by Thode (2002), and may help reducing visual
bias caused by the orthogonal distances from P-P points to the reference
line.
|
... |
Other arguments passed on to layer() 's params argument. These
arguments broadly fall into one of 4 categories below. Notably, further
arguments to the position argument, or aesthetics that are required
can not be passed through ... . Unknown arguments that are not part
of the 4 categories below are ignored.
Static aesthetics that are not mapped to a scale, but are at a fixed
value and apply to the layer as a whole. For example, colour = "red"
or linewidth = 3 . The geom's documentation has an Aesthetics
section that lists the available options. The 'required' aesthetics
cannot be passed on to the params . Please note that while passing
unmapped aesthetics as vectors is technically possible, the order and
required length is not guaranteed to be parallel to the input data.
When constructing a layer using
a stat_*() function, the ... argument can be used to pass on
parameters to the geom part of the layer. An example of this is
stat_density(geom = "area", outline.type = "both") . The geom's
documentation lists which parameters it can accept.
Inversely, when constructing a layer using a
geom_*() function, the ... argument can be used to pass on parameters
to the stat part of the layer. An example of this is
geom_area(stat = "density", adjust = 0.5) . The stat's documentation
lists which parameters it can accept.
The key_glyph argument of layer() may also be passed on through
... . This can be one of the functions described as
key glyphs, to change the display of the layer in the legend.
|
Examples
# generate random Normal data
set.seed(0)
smp <- data.frame(norm = rnorm(100))
# Normal P-P plot of Normal data
gg <- ggplot(data = smp, mapping = aes(sample = norm)) +
stat_pp_line() +
stat_pp_point() +
labs(x = "Probability Points", y = "Cumulative Probability")
gg
# Shifted Normal P-P plot of Normal data
dp <- list(mean = 1.5)
gg <- ggplot(data = smp, mapping = aes(sample = norm)) +
stat_pp_line() +
stat_pp_point(dparams = dp) +
labs(x = "Probability Points", y = "Cumulative Probability")
gg
# Normal P-P plot of mean ozone levels (airquality dataset)
dp <- list(mean = 38, sd = 27)
gg <- ggplot(data = airquality, mapping = aes(sample = Ozone)) +
stat_pp_line() +
stat_pp_point(dparams = dp) +
labs(x = "Probability Points", y = "Cumulative Probability")
gg
Probability-probability points
Description
Draws probability-probability points.
Usage
stat_pp_point(
mapping = NULL,
data = NULL,
geom = "point",
position = "identity",
na.rm = TRUE,
show.legend = NA,
inherit.aes = TRUE,
distribution = "norm",
dparams = list(),
detrend = FALSE,
down.sample = NULL,
...
)
Arguments
mapping |
Set of aesthetic mappings created by aes() . If specified and
inherit.aes = TRUE (the default), it is combined with the default mapping
at the top level of the plot. You must supply mapping if there is no plot
mapping.
|
data |
The data to be displayed in this layer. There are three
options:
If NULL , the default, the data is inherited from the plot
data as specified in the call to ggplot() .
A data.frame , or other object, will override the plot
data. All objects will be fortified to produce a data frame. See
fortify() for which variables will be created.
A function will be called with a single argument,
the plot data. The return value must be a data.frame , and
will be used as the layer data. A function can be created
from a formula (e.g. ~ head(.x, 10) ).
|
geom |
The geometric object to use to display the data for this layer.
When using a stat_*() function to construct a layer, the geom argument
can be used to override the default coupling between stats and geoms. The
geom argument accepts the following:
A Geom ggproto subclass, for example GeomPoint .
A string naming the geom. To give the geom as a string, strip the
function name of the geom_ prefix. For example, to use geom_point() ,
give the geom as "point" .
For more information and other ways to specify the geom, see the
layer geom documentation.
|
position |
A position adjustment to use on the data for this layer. This
can be used in various ways, including to prevent overplotting and
improving the display. The position argument accepts the following:
The result of calling a position function, such as position_jitter() .
This method allows for passing extra arguments to the position.
A string naming the position adjustment. To give the position as a
string, strip the function name of the position_ prefix. For example,
to use position_jitter() , give the position as "jitter" .
For more information and other ways to specify the position, see the
layer position documentation.
|
na.rm |
If FALSE , the default, missing values are removed with
a warning. If TRUE , missing values are silently removed.
|
show.legend |
logical. Should this layer be included in the legends?
NA , the default, includes if any aesthetics are mapped.
FALSE never includes, and TRUE always includes.
It can also be a named logical vector to finely select the aesthetics to
display. To include legend keys for all levels, even
when no data exists, use TRUE . If NA , all levels are shown in legend,
but unobserved levels are omitted.
|
inherit.aes |
If FALSE, overrides the default aesthetics, rather than
combining with them. This is most useful for helper functions that define
both data and aesthetics and shouldn't inherit behaviour from the default
plot specification
|
distribution |
Character. Theoretical probability distribution function
to use. Do not provide the full distribution function name (e.g.,
"dnorm" ). Instead, just provide its shortened name (e.g.,
"norm" ). If you wish to provide a custom distribution, you may do so
by first creating the density, quantile, and random functions following the
standard nomenclature from the stats package (i.e., for
"custom" , create the dcustom , pcustom ,
qcustom , and rcustom functions).
|
dparams |
List of additional parameters passed on to the previously
chosen distribution function. If an empty list is provided (default)
then the distributional parameters are estimated via MLE. MLE for custom
distributions is currently not supported, so you must provide the
appropriate dparams in that case.
|
detrend |
Logical. Should the plot objects be detrended? If TRUE ,
the objects will be detrended according to the default identity P-P line.
This procedure was described by Thode (2002), and may help reducing visual
bias caused by the orthogonal distances from P-P points to the reference
line.
|
down.sample |
Integer specifying how many points you want to sample
in a reduced sample (i.e., a down sample). The default value is NULL
indicating no downsampling.
|
... |
Other arguments passed on to layer() 's params argument. These
arguments broadly fall into one of 4 categories below. Notably, further
arguments to the position argument, or aesthetics that are required
can not be passed through ... . Unknown arguments that are not part
of the 4 categories below are ignored.
Static aesthetics that are not mapped to a scale, but are at a fixed
value and apply to the layer as a whole. For example, colour = "red"
or linewidth = 3 . The geom's documentation has an Aesthetics
section that lists the available options. The 'required' aesthetics
cannot be passed on to the params . Please note that while passing
unmapped aesthetics as vectors is technically possible, the order and
required length is not guaranteed to be parallel to the input data.
When constructing a layer using
a stat_*() function, the ... argument can be used to pass on
parameters to the geom part of the layer. An example of this is
stat_density(geom = "area", outline.type = "both") . The geom's
documentation lists which parameters it can accept.
Inversely, when constructing a layer using a
geom_*() function, the ... argument can be used to pass on parameters
to the stat part of the layer. An example of this is
geom_area(stat = "density", adjust = 0.5) . The stat's documentation
lists which parameters it can accept.
The key_glyph argument of layer() may also be passed on through
... . This can be one of the functions described as
key glyphs, to change the display of the layer in the legend.
|
References
Examples
# generate random Normal data
set.seed(0)
smp <- data.frame(norm = rnorm(100))
# Normal P-P plot of Normal data
gg <- ggplot(data = smp, mapping = aes(sample = norm)) +
stat_pp_point() +
labs(x = "Probability Points", y = "Cumulative Probability")
gg
# Shifted Normal P-P plot of Normal data
dp <- list(mean = 1.5)
gg <- ggplot(data = smp, mapping = aes(sample = norm)) +
stat_pp_point(dparams = dp) +
labs(x = "Probability Points", y = "Cumulative Probability")
gg
# Normal P-P plot of mean ozone levels (airquality dataset)
dp <- list(mean = 38, sd = 27)
gg <- ggplot(data = airquality, mapping = aes(sample = Ozone)) +
stat_pp_point(dparams = dp) +
labs(x = "Probability Points", y = "Cumulative Probability")
gg
Quantile-quantile lines
Description
Draws a quantile-quantile line, with an additional detrend option.
Usage
stat_qq_line(
mapping = NULL,
data = NULL,
geom = "path",
position = "identity",
na.rm = TRUE,
show.legend = NA,
inherit.aes = TRUE,
distribution = "norm",
dparams = list(),
detrend = FALSE,
identity = FALSE,
qtype = 7,
qprobs = c(0.25, 0.75),
...
)
Arguments
mapping |
Set of aesthetic mappings created by aes() . If specified and
inherit.aes = TRUE (the default), it is combined with the default mapping
at the top level of the plot. You must supply mapping if there is no plot
mapping.
|
data |
The data to be displayed in this layer. There are three
options:
If NULL , the default, the data is inherited from the plot
data as specified in the call to ggplot() .
A data.frame , or other object, will override the plot
data. All objects will be fortified to produce a data frame. See
fortify() for which variables will be created.
A function will be called with a single argument,
the plot data. The return value must be a data.frame , and
will be used as the layer data. A function can be created
from a formula (e.g. ~ head(.x, 10) ).
|
geom |
The geometric object to use to display the data for this layer.
When using a stat_*() function to construct a layer, the geom argument
can be used to override the default coupling between stats and geoms. The
geom argument accepts the following:
A Geom ggproto subclass, for example GeomPoint .
A string naming the geom. To give the geom as a string, strip the
function name of the geom_ prefix. For example, to use geom_point() ,
give the geom as "point" .
For more information and other ways to specify the geom, see the
layer geom documentation.
|
position |
A position adjustment to use on the data for this layer. This
can be used in various ways, including to prevent overplotting and
improving the display. The position argument accepts the following:
The result of calling a position function, such as position_jitter() .
This method allows for passing extra arguments to the position.
A string naming the position adjustment. To give the position as a
string, strip the function name of the position_ prefix. For example,
to use position_jitter() , give the position as "jitter" .
For more information and other ways to specify the position, see the
layer position documentation.
|
na.rm |
If FALSE , the default, missing values are removed with
a warning. If TRUE , missing values are silently removed.
|
show.legend |
logical. Should this layer be included in the legends?
NA , the default, includes if any aesthetics are mapped.
FALSE never includes, and TRUE always includes.
It can also be a named logical vector to finely select the aesthetics to
display. To include legend keys for all levels, even
when no data exists, use TRUE . If NA , all levels are shown in legend,
but unobserved levels are omitted.
|
inherit.aes |
If FALSE, overrides the default aesthetics, rather than
combining with them. This is most useful for helper functions that define
both data and aesthetics and shouldn't inherit behaviour from the default
plot specification
|
distribution |
Character. Theoretical probability distribution function
to use. Do not provide the full distribution function name (e.g.,
"dnorm" ). Instead, just provide its shortened name (e.g.,
"norm" ). If you wish to provide a custom distribution, you may do so
by first creating the density, quantile, and random functions following the
standard nomenclature from the stats package (i.e., for
"custom" , create the dcustom , pcustom ,
qcustom , and rcustom functions).
|
dparams |
List of additional parameters passed on to the previously
chosen distribution function. If an empty list is provided (default)
then the distributional parameters are estimated via MLE. MLE for custom
distributions is currently not supported, so you must provide the
appropriate dparams in that case.
|
detrend |
Logical. Should the plot objects be detrended? If TRUE ,
the objects will be detrended according to the reference Q-Q line. This
procedure was described by Thode (2002), and may help reducing visual bias
caused by the orthogonal distances from Q-Q points to the reference line.
|
identity |
Logical. Should an identity line be used as the reference
line? If TRUE , the identity line is used. If FALSE (default),
the commonly-used Q-Q line that intercepts two data quantiles specified in
qprobs is used. Please notice that the chosen reference line will
also be used for the detrending procedure, if detrend = TRUE .
|
qtype |
Integer between 1 and 9. Only used if detrend = TRUE and
identity = FALSE . Type of the quantile algorithm to be used by the
quantile function to construct the Q-Q line.
|
qprobs |
Numeric vector of length two. Only used if detrend =
TRUE and identity = FALSE . Represents the quantiles used by the
quantile function to construct the Q-Q line.
|
... |
Other arguments passed on to layer() 's params argument. These
arguments broadly fall into one of 4 categories below. Notably, further
arguments to the position argument, or aesthetics that are required
can not be passed through ... . Unknown arguments that are not part
of the 4 categories below are ignored.
Static aesthetics that are not mapped to a scale, but are at a fixed
value and apply to the layer as a whole. For example, colour = "red"
or linewidth = 3 . The geom's documentation has an Aesthetics
section that lists the available options. The 'required' aesthetics
cannot be passed on to the params . Please note that while passing
unmapped aesthetics as vectors is technically possible, the order and
required length is not guaranteed to be parallel to the input data.
When constructing a layer using
a stat_*() function, the ... argument can be used to pass on
parameters to the geom part of the layer. An example of this is
stat_density(geom = "area", outline.type = "both") . The geom's
documentation lists which parameters it can accept.
Inversely, when constructing a layer using a
geom_*() function, the ... argument can be used to pass on parameters
to the stat part of the layer. An example of this is
geom_area(stat = "density", adjust = 0.5) . The stat's documentation
lists which parameters it can accept.
The key_glyph argument of layer() may also be passed on through
... . This can be one of the functions described as
key glyphs, to change the display of the layer in the legend.
|
References
Examples
# generate random Normal data
set.seed(0)
smp <- data.frame(norm = rnorm(100))
# Normal Q-Q plot of Normal data
gg <- ggplot(data = smp, mapping = aes(sample = norm)) +
stat_qq_line() +
stat_qq_point() +
labs(x = "Theoretical Quantiles", y = "Sample Quantiles")
gg
# Exponential Q-Q plot of mean ozone levels (airquality dataset)
di <- "exp"
dp <- list(rate = 1)
gg <- ggplot(data = airquality, mapping = aes(sample = Ozone)) +
stat_qq_line(distribution = di, dparams = dp) +
stat_qq_point(distribution = di, dparams = dp) +
labs(x = "Theoretical Quantiles", y = "Sample Quantiles")
gg
# Detrended Exponential Q-Q plot of mean ozone levels
di <- "exp"
dp <- list(rate = 1)
de <- TRUE
gg <- ggplot(data = airquality, mapping = aes(sample = Ozone)) +
stat_qq_line(distribution = di, detrend = de) +
stat_qq_point(distribution = di, detrend = de) +
labs(x = "Theoretical Quantiles", y = "Sample Quantiles")
gg
Quantile-quantile points
Description
Draws quantile-quantile points, with an additional detrend option.
Usage
stat_qq_point(
mapping = NULL,
data = NULL,
geom = "point",
position = "identity",
na.rm = TRUE,
show.legend = NA,
inherit.aes = TRUE,
distribution = "norm",
dparams = list(),
detrend = FALSE,
identity = FALSE,
qtype = 7,
qprobs = c(0.25, 0.75),
down.sample = NULL,
...
)
Arguments
mapping |
Set of aesthetic mappings created by aes() . If specified and
inherit.aes = TRUE (the default), it is combined with the default mapping
at the top level of the plot. You must supply mapping if there is no plot
mapping.
|
data |
The data to be displayed in this layer. There are three
options:
If NULL , the default, the data is inherited from the plot
data as specified in the call to ggplot() .
A data.frame , or other object, will override the plot
data. All objects will be fortified to produce a data frame. See
fortify() for which variables will be created.
A function will be called with a single argument,
the plot data. The return value must be a data.frame , and
will be used as the layer data. A function can be created
from a formula (e.g. ~ head(.x, 10) ).
|
geom |
The geometric object to use to display the data for this layer.
When using a stat_*() function to construct a layer, the geom argument
can be used to override the default coupling between stats and geoms. The
geom argument accepts the following:
A Geom ggproto subclass, for example GeomPoint .
A string naming the geom. To give the geom as a string, strip the
function name of the geom_ prefix. For example, to use geom_point() ,
give the geom as "point" .
For more information and other ways to specify the geom, see the
layer geom documentation.
|
position |
A position adjustment to use on the data for this layer. This
can be used in various ways, including to prevent overplotting and
improving the display. The position argument accepts the following:
The result of calling a position function, such as position_jitter() .
This method allows for passing extra arguments to the position.
A string naming the position adjustment. To give the position as a
string, strip the function name of the position_ prefix. For example,
to use position_jitter() , give the position as "jitter" .
For more information and other ways to specify the position, see the
layer position documentation.
|
na.rm |
If FALSE , the default, missing values are removed with
a warning. If TRUE , missing values are silently removed.
|
show.legend |
logical. Should this layer be included in the legends?
NA , the default, includes if any aesthetics are mapped.
FALSE never includes, and TRUE always includes.
It can also be a named logical vector to finely select the aesthetics to
display. To include legend keys for all levels, even
when no data exists, use TRUE . If NA , all levels are shown in legend,
but unobserved levels are omitted.
|
inherit.aes |
If FALSE, overrides the default aesthetics, rather than
combining with them. This is most useful for helper functions that define
both data and aesthetics and shouldn't inherit behaviour from the default
plot specification
|
distribution |
Character. Theoretical probability distribution function
to use. Do not provide the full distribution function name (e.g.,
"dnorm" ). Instead, just provide its shortened name (e.g.,
"norm" ). If you wish to provide a custom distribution, you may do so
by first creating the density, quantile, and random functions following the
standard nomenclature from the stats package (i.e., for
"custom" , create the dcustom , pcustom ,
qcustom , and rcustom functions).
|
dparams |
List of additional parameters passed on to the previously
chosen distribution function. If an empty list is provided (default)
then the distributional parameters are estimated via MLE. MLE for custom
distributions is currently not supported, so you must provide the
appropriate dparams in that case.
|
detrend |
Logical. Should the plot objects be detrended? If TRUE ,
the objects will be detrended according to the reference Q-Q line. This
procedure was described by Thode (2002), and may help reducing visual bias
caused by the orthogonal distances from Q-Q points to the reference line.
|
identity |
Logical. Only used if detrend = TRUE . Should an
identity line be used as the reference line for the plot detrending? If
TRUE , the points will be detrended according to the reference
identity line. If FALSE (default), the commonly-used Q-Q line that
intercepts two data quantiles specified in qprobs is used.
|
qtype |
Integer between 1 and 9. Only used if detrend = TRUE and
identity = FALSE . Type of the quantile algorithm to be used by the
quantile function to construct the Q-Q line.
|
qprobs |
Numeric vector of length two. Only used if detrend =
TRUE and identity = FALSE . Represents the quantiles used by the
quantile function to construct the Q-Q line.
|
down.sample |
Integer specifying how many points you want to sample
in a reduced sample (i.e., a down sample). The default value is NULL
indicating no downsampling.
|
... |
Other arguments passed on to layer() 's params argument. These
arguments broadly fall into one of 4 categories below. Notably, further
arguments to the position argument, or aesthetics that are required
can not be passed through ... . Unknown arguments that are not part
of the 4 categories below are ignored.
Static aesthetics that are not mapped to a scale, but are at a fixed
value and apply to the layer as a whole. For example, colour = "red"
or linewidth = 3 . The geom's documentation has an Aesthetics
section that lists the available options. The 'required' aesthetics
cannot be passed on to the params . Please note that while passing
unmapped aesthetics as vectors is technically possible, the order and
required length is not guaranteed to be parallel to the input data.
When constructing a layer using
a stat_*() function, the ... argument can be used to pass on
parameters to the geom part of the layer. An example of this is
stat_density(geom = "area", outline.type = "both") . The geom's
documentation lists which parameters it can accept.
Inversely, when constructing a layer using a
geom_*() function, the ... argument can be used to pass on parameters
to the stat part of the layer. An example of this is
geom_area(stat = "density", adjust = 0.5) . The stat's documentation
lists which parameters it can accept.
The key_glyph argument of layer() may also be passed on through
... . This can be one of the functions described as
key glyphs, to change the display of the layer in the legend.
|
References
Examples
# generate random Normal data
set.seed(0)
smp <- data.frame(norm = rnorm(100))
# Normal Q-Q plot of simulated Normal data
gg <- ggplot(data = smp, mapping = aes(sample = norm)) +
stat_qq_point() +
labs(x = "Theoretical Quantiles", y = "Sample Quantiles")
gg
# Exponential Q-Q plot of mean ozone levels (airquality dataset)
di <- "exp"
dp <- list(rate = 1)
gg <- ggplot(data = airquality, mapping = aes(sample = Ozone)) +
stat_qq_point(distribution = di, dparams = dp) +
labs(x = "Theoretical Quantiles", y = "Sample Quantiles")
gg