### 2D density plots

tags/v0.1.1
hrbrmstr 8 years ago
parent
commit
2503e1b85b
10 changed files with 242 additions and 8 deletions
1. 2
DESCRIPTION
2. 4
NAMESPACE
3. 105
R/geom_bkde2d.r
4. 21
5. 34
6. BIN
7. BIN
8. 57
man/geom_bkde2d.Rd
9. 4
man/ggalt-ggproto.Rd
10. 23
man/stat_bkde2d.Rd

#### 2 DESCRIPTION View File

 @ -1,6 +1,6 @@ Package: ggalt Title: Extra Geoms, Stats and Coords for 'ggplot2' Version: 0.0.1.9001 Version: 0.0.2.9000 Authors@R: c(person("Bob", "Rudis", email = "bob@rudis.net", role = c("aut", "cre"))) Description: A package contains additional geoms, coords and stats for the revamped (late 2015) version of ggplot2. Depends: R (>= 3.0.0), ggplot2 (>= 1.0.1.9003)

#### 4 NAMESPACE View File

 @ -1,12 +1,16 @@ # Generated by roxygen2 (4.1.1): do not edit by hand export(GeomBkde) export(GeomBkde2d) export(GeomXspline) export(StatBkde) export(StatBkde2d) export(StatXspline) export(geom_bkde) export(geom_bkde2d) export(geom_xspline) export(stat_bkde) export(stat_bkde2d) export(stat_xspline) import(KernSmooth) import(dplyr)

#### 105 R/geom_bkde2d.r View File

 @ -0,0 +1,105 @@ #' Contours from a 2d density estimate. #' #' @inheritParams ggplot2::geom_point #' @inheritParams ggplot2::geom_path #' @export geom_bkde2d <- function(mapping = NULL, data = NULL, stat = "bkde2d", position = "identity", bandwidth, range.x=NULL, lineend = "butt", contour=TRUE, linejoin = "round", linemitre = 1, show.legend = NA, inherit.aes = TRUE, ...) { layer( data = data, mapping = mapping, stat = stat, geom = GeomBkde2d, position = position, show.legend = show.legend, inherit.aes = inherit.aes, params = list( lineend = lineend, linejoin = linejoin, linemitre = linemitre, bandwidth = bandwidth, range.x = range.x, ... ) ) } #' @rdname ggalt-ggproto #' @format NULL #' @usage NULL #' @export GeomBkde2d <- ggproto("GeomBkde2d", GeomPath, default_aes = aes(colour = "#3366FF", size = 0.5, linetype = 1, alpha = NA) ) #' 2D density #' #' @export #' @param contour If \code{TRUE}, contour the results of the 2d density #' estimation #' @section Computed variables: #' Same as \code{\link{stat_contour}} stat_bkde2d <- function(mapping = NULL, data = NULL, geom = "density2d", position = "identity", contour = TRUE, bandwidth, grid_size=c(51, 51), range.x=NULL, truncate=TRUE, show.legend = NA, inherit.aes = TRUE, ...) { layer( data = data, mapping = mapping, stat = StatBkde2d, geom = geom, position = position, show.legend = show.legend, inherit.aes = inherit.aes, params = list( bandwidth = bandwidth, grid_size = grid_size, range.x = range.x, truncate = truncate, contour = contour, ... ) ) } #' @rdname ggalt-ggproto #' @format NULL #' @usage NULL #' @export StatBkde2d <- ggproto("StatBkde2d", Stat, default_aes = aes(colour = "#3366FF", size = 0.5), required_aes = c("x", "y"), compute_group = function(data, scales, contour=TRUE, bandwidth, grid_size=c(51, 51), range.x=NULL, truncate=TRUE) { if (is.null(range.x)) range.x <- list(range(data$x), range(data$y)) dens <- KernSmooth::bkde2D( as.matrix(data.frame(x=data$x, y=data$y)), bandwidth, grid_size, range.x, truncate ) df <- data.frame(expand.grid(x = dens$x1, y = dens$x2), z = as.vector(dens$fhat)) df$group <- data$group[1] if (contour) { StatContour$compute_panel(df, scales) } else { names(df) <- c("x", "y", "density", "group") df$level <- 1 df$piece <- 1 df } } )

 @ -21,7 +21,8 @@ A package containing additional geoms, coords and stats for the revamped (late 2 of ggplot2. The first two forays into this brave, new ggplot2 world are _splines_! and being able to use the (much better) KernSmooth::bkde for density plots. use the (much better) KernSmooth::bkde for density plots. Support for KernSmooth::bkde2D is a WIP. *NOTE* @ -33,10 +34,12 @@ The following functions are implemented: - stat_xspline : Connect control points/observations with an X-spline - geom_bkde : Display a smooth density estimate (uses KernSmooth::bkde) - stat_bkde : Display a smooth density estimate (uses KernSmooth::bkde) - geom_bkde2d : Contours from a 2d density estimate. (uses KernSmooth::bkde2D) **WIP** - stat_bkde2d : Contours from a 2d density estimate. (uses KernSmooth::bkde2D) **WIP** ### News - Version 0.0.1.9000 released - Version 0.0.2.9000 released ### Installation @ -113,6 +116,20 @@ ggplot(geyser, aes(x=duration)) + ggplot(geyser, aes(x=duration)) + geom_bkde(bandwidth=0.25) # 2D KernSmooth::bkde2D plots are a WIP geyser_dat <- data.frame(x=geyser$duration, y=geyser$waiting) ggplot(geyser_dat, aes(x, y)) + geom_point() + geom_bkde2d(bandwidth=c(0.7, 7)) + xlim(0, 6) + ylim(35, 120) ggplot(geyser_dat, aes(x, y)) + geom_point() + stat_bkde2d(bandwidth=c(0.7, 7)) + xlim(0, 6) + ylim(35, 120)  ### Test Results

 @ -3,7 +3,7 @@ A package containing additional geoms, coords and stats for the revamped (late 2015) version of ggplot2. The first two forays into this brave, new ggplot2 world are *splines*! and being able to use the (much better) KernSmooth::bkde for density plots. The first two forays into this brave, new ggplot2 world are *splines*! and being able to use the (much better) KernSmooth::bkde for density plots. Support for KernSmooth::bkde2D is a WIP. *NOTE* @ -15,10 +15,12 @@ The following functions are implemented: - stat_xspline : Connect control points/observations with an X-spline - geom_bkde : Display a smooth density estimate (uses KernSmooth::bkde) - stat_bkde : Display a smooth density estimate (uses KernSmooth::bkde) - geom_bkde2d : Contours from a 2d density estimate. (uses KernSmooth::bkde2D) **WIP** - stat_bkde2d : Contours from a 2d density estimate. (uses KernSmooth::bkde2D) **WIP** ### News - Version 0.0.1.9000 released - Version 0.0.2.9000 released ### Installation @ -36,7 +38,7 @@ library(ggalt) # current verison packageVersion("ggalt") #> [1] '0.0.1.9001' #> [1] '0.0.2.9000' set.seed(1492) dat <- data.frame(x=c(1:10, 1:10, 1:10), @ -141,6 +143,30 @@ ggplot(geyser, aes(x=duration)) +  r # 2D KernSmooth::bkde2D plots are a WIP geyser_dat <- data.frame(x=geyser$duration, y=geyser$waiting) ggplot(geyser_dat, aes(x, y)) + geom_point() + geom_bkde2d(bandwidth=c(0.7, 7)) + xlim(0, 6) + ylim(35, 120)   r ggplot(geyser_dat, aes(x, y)) + geom_point() + stat_bkde2d(bandwidth=c(0.7, 7)) + xlim(0, 6) + ylim(35, 120)  ### Test Results  r @ -148,7 +174,7 @@ library(ggalt) library(testthat) date() #> [1] "Tue Sep 8 16:16:44 2015" #> [1] "Tue Sep 8 17:20:02 2015" test_dir("tests/") #> testthat results ========================================================================================================

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#### 57 man/geom_bkde2d.Rd View File

 @ -0,0 +1,57 @@ % Generated by roxygen2 (4.1.1): do not edit by hand % Please edit documentation in R/geom_bkde2d.r \name{geom_bkde2d} \alias{geom_bkde2d} \title{Contours from a 2d density estimate.} \usage{ geom_bkde2d(mapping = NULL, data = NULL, stat = "bkde2d", position = "identity", bandwidth, range.x = NULL, lineend = "butt", contour = TRUE, linejoin = "round", linemitre = 1, show.legend = NA, inherit.aes = TRUE, ...) } \arguments{ \item{mapping}{Set of aesthetic mappings created by \code{\link{aes}} or \code{\link{aes_}}. If specified and \code{inherit.aes = TRUE} (the default), is combined with the default mapping at the top level of the plot. You only need to supply \code{mapping} if there isn't a mapping defined for the plot.} \item{data}{A data frame. If specified, overrides the default data frame defined at the top level of the plot.} \item{stat}{The statistical transformation to use on the data for this layer, as a string.} \item{position}{Position adjustment, either as a string, or the result of a call to a position adjustment function.} \item{lineend}{Line end style (round, butt, square)} \item{linejoin}{Line join style (round, mitre, bevel)} \item{linemitre}{Line mitre limit (number greater than 1)} \item{show.legend}{logical. Should this layer be included in the legends? \code{NA}, the default, includes if any aesthetics are mapped. \code{FALSE} never includes, and \code{TRUE} always includes.} \item{inherit.aes}{If \code{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, e.g. \code{\link{borders}}.} \item{...}{other arguments passed on to \code{\link{layer}}. There are three types of arguments you can use here: \itemize{ \item Aesthetics: to set an aesthetic to a fixed value, like \code{color = "red"} or \code{size = 3}. \item Other arguments to the layer, for example you override the default \code{stat} associated with the layer. \item Other arguments passed on to the stat. }} } \description{ Contours from a 2d density estimate. }

#### 4 man/ggalt-ggproto.Rd View File

 @ -1,10 +1,12 @@ % Generated by roxygen2 (4.1.1): do not edit by hand % Please edit documentation in R/geom_bkde.r, R/geom_xspline.r % Please edit documentation in R/geom_bkde.r, R/geom_bkde2d.r, R/geom_xspline.r \docType{data} \name{GeomBkde} \alias{GeomBkde} \alias{GeomBkde2d} \alias{GeomXspline} \alias{StatBkde} \alias{StatBkde2d} \alias{StatXspline} \title{GeomXspline} \description{

#### 23 man/stat_bkde2d.Rd View File

 @ -0,0 +1,23 @@ % Generated by roxygen2 (4.1.1): do not edit by hand % Please edit documentation in R/geom_bkde2d.r \name{stat_bkde2d} \alias{stat_bkde2d} \title{2D density} \usage{ stat_bkde2d(mapping = NULL, data = NULL, geom = "density2d", position = "identity", contour = TRUE, bandwidth, grid_size = c(51, 51), range.x = NULL, truncate = TRUE, show.legend = NA, inherit.aes = TRUE, ...) } \arguments{ \item{contour}{If \code{TRUE}, contour the results of the 2d density estimation} } \description{ 2D density } \section{Computed variables}{ Same as \code{\link{stat_contour}} }