Merge pull request #11 from evanbiederstedt/cran_review_fix

CRAN version 0.1.8

.Rbuildignore

@@ -1,2 +1,5 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
+.travis.yml
+CHANGELOG.md
+^LICENSE\.md$

.gitignore

@@ -2,3 +2,4 @@
 .Rhistory
 .RData
 .Ruserdata
+ggrastr*.tar.gz

.travis.yml

@@ -0,0 +1,12 @@
+language: r
+
+## minimal travis config
+## https://docs.travis-ci.com/user/languages/r/
+## https://towardsdatascience.com/travis-ci-for-r-advanced-guide-719cb2d9e0e5
+
+## no tests, coverage
+## check as CRAN
+
+script:
+  - R CMD build . --compact-vignettes=gs+qpdf
+  - R CMD check *tar.gz --as-cran 

CHANGELOG.md

@@ -1,4 +1,9 @@
 # Changelog
+
+## [0.1.8] - 2020-06-19
+* Revisions for first version on CRAN. 
+* Documentation revisions, changes to the vignettes
+
 ## [0.1.7] - 2018-12-02
 ### Fixed
 * All pararmeters `width`, `hight` and `dpi` renamed to `raster.width`, `raster.hight` and `raster.dpi` correspondingly to avoid name conflicts.

DESCRIPTION

@@ -1,20 +1,25 @@
 Package: ggrastr
 Type: Package
-Title: Raster layers for ggplot2
-Version: 0.1.7
-Authors@R: c(person("Viktor", "Petukhov", email = "[email protected]", role = c("cre", "aut")))
-Description: Raster geoms for ggplot2
-License: MIT
+Title: Raster Layers for 'ggplot2'
+Version: 0.1.8
+Authors@R: c(person("Viktor", "Petukhov", email = "[email protected]", role = c("aut", "cph")), person("Evan", "Biederstedt", email = "[email protected]", role=c("cre", "aut")))
+Description: Provides a set of geoms to rasterize only specific layers of the plot while simultaneously keeping all labels and text in vector format. This allows users to keep plots within the reasonable size limit without loosing vector properties of the scale-sensitive information. 
+License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
 Imports:
   ggplot2 (>= 2.1.0),
   Cairo (>= 1.5.9),
+  ggbeeswarm
 Depends:
   R (>= 3.2.2)
-RoxygenNote: 6.1.0
+RoxygenNote: 7.1.0
 Suggests:
-  ggbeeswarm,
-  knitr,
-  rmarkdown
+  rmarkdown,
+  knitr
 VignetteBuilder: knitr
+URL: https://github.com/VPetukhov/ggrastr
+BugReports: https://github.com/VPetukhov/ggrastr/issues
+NeedsCompilation: no
+Author: Viktor Petukhov [aut, cph], Evan Biederstedt [cre, aut]
+Maintainer: Evan Biederstedt <[email protected]>

LICENSE

@@ -1,21 +1,2 @@
-MIT License
-
-Copyright (c) 2017 Viktor Petukhov
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+YEAR: 2020
+COPYRIGHT HOLDER: Viktor Petukhov <[email protected]>

LICENSE.md

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2017 Viktor Petukhov
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

NAMESPACE

@@ -6,3 +6,9 @@ export(geom_point_rast)
 export(geom_quasirandom_rast)
 export(geom_tile_rast)
 export(theme_pdf)
+import(ggbeeswarm)
+import(ggplot2)
+importFrom(grDevices,dev.cur)
+importFrom(grDevices,dev.off)
+importFrom(grDevices,dev.set)
+importFrom(graphics,par)

R/geom-beeswarm-rast.R

@@ -1,13 +1,21 @@
 #' This geom is similar to \code{\link[ggbeeswarm]{geom_beeswarm}}, but creates a raster layer
 #'
 #' @inheritParams geom_point_rast
-#' @inheritParams ggbeeswarm::position_beeswarm
-#' @inheritSection ggplot2::geom_point Aesthetics
+#'
+#' @import ggplot2
+#' @import ggbeeswarm
+#' @param priority Method used to perform point layout (see ggbeeswarm::position_beeswarm)
+#' @param cex Scaling for adjusting point spacing (see ggbeeswarm::position_beeswarm)
+#' @param groupOnX Should jitter be added to the x axis if TRUE or y axis if FALSE (the default NULL causes the function to guess which axis is the categorical one based on the number of unique entries in each) Refer to see ggbeeswarm::position_beeswarm 
+#' @param dodge.width Amount by which points from different aesthetic groups will be dodged. This requires that one of the aesthetics is a factor. (see ggbeeswarm::position_beeswarm)
+#' @return geom_beeswarm plot with rasterized layer
 #'
 #' @examples
+#' library(ggplot2)
+#' library(ggrastr)
+#'
 #' ggplot(mtcars) + geom_beeswarm_rast(aes(x = factor(cyl), y = mpg), raster.dpi = 600, cex = 1.5)
 #'
-
 #' @export
 geom_beeswarm_rast <- function(
   mapping = NULL,
@@ -25,10 +33,6 @@ geom_beeswarm_rast <- function(
   raster.width=NULL, raster.height=NULL, raster.dpi=300
 ) {
 
-  if (!requireNamespace('ggbeeswarm', quietly = T)) {
-    stop('Install \"ggbeeswarm\" to use this function', call. = F)
-  }
-
   position <- ggbeeswarm::position_beeswarm(priority = priority, cex = cex,
                                             groupOnX = groupOnX, dodge.width = dodge.width)
 

R/geom-boxplot-jitter.R

@@ -70,9 +70,15 @@ GeomBoxplotJitter <- ggplot2::ggproto("GeomBoxplotJitter",
 #' @param raster.dpi Resolution of the rastered image. Ignored if \code{raster == FALSE}.
 #' @param raster.width Width of the result image (in inches). Default: deterined by the current device parameters. Ignored if \code{raster == FALSE}.
 #' @param raster.height Height of the result image (in inches). Default: deterined by the current device parameters. Ignored if \code{raster == FALSE}.
+#' @return geom_boxplot plot with rasterized layer
 #'
 #' @examples
-#' ggplot() + geom_boxplot_jitter(aes(y=rt(1000, df=3), x=as.factor(1:1000 %% 2)), outlier.jitter.width = 0.1, raster = T)
+#' library(ggplot2)
+#' library(ggrastr)
+#'
+#' yvalues = rt(1000, df=3)
+#' xvalues = as.factor(1:1000 %% 2)
+#' ggplot() + geom_boxplot_jitter(aes(y=yvalues, x=xvalues), outlier.jitter.width = 0.1, raster = TRUE)
 #'
 #' @export
 geom_boxplot_jitter <- function(mapping = NULL, data = NULL,

R/geom-point-rast.R

@@ -1,3 +1,5 @@
+#' @importFrom grDevices dev.cur dev.off dev.set
+#' @importFrom graphics par
 DrawGeomPointRast <- function(data, panel_params, coord, na.rm = FALSE, raster.width=NULL, raster.height=NULL, raster.dpi=300) {
   if (is.null(raster.width)) {
     raster.width <- par('fin')[1]
@@ -36,11 +38,16 @@ GeomPointRast <- ggplot2::ggproto(
 #' @inheritParams ggplot2::geom_point
 #' @inheritSection ggplot2::geom_point Aesthetics
 #'
+#' @import ggplot2
 #' @param raster.width Width of the result image (in inches). Default: deterined by the current device parameters.
 #' @param raster.height Height of the result image (in inches). Default: deterined by the current device parameters.
 #' @param raster.dpi Resolution of the result image.
+#' @return geom_point plot with rasterized layer
 #'
 #' @examples
+#' library(ggplot2)
+#' library(ggrastr)
+#'
 #' ggplot() + geom_point_rast(aes(x=rnorm(1000), y=rnorm(1000)), raster.dpi=600)
 #'
 #' @export

R/geom-quasirandom-rast.R

@@ -3,35 +3,34 @@
 #' @inheritParams geom_point_rast
 #' @inheritParams ggbeeswarm::position_quasirandom
 #' @inheritSection ggplot2::geom_point Aesthetics
+#' @return geom_quasirandom plot with rasterized layer
 #'
 #' @examples
+#' library(ggplot2)
+#' library(ggrastr)
+#'
 #' ggplot(mtcars) + geom_quasirandom_rast(aes(x = factor(cyl), y = mpg), raster.dpi = 600)
 #'
-
 #' @export
 geom_quasirandom_rast <- function(
   mapping = NULL,
   data = NULL,
   stat = 'identity',
   position = 'quasirandom',
-  width=NULL,
+  width = NULL,
   varwidth = FALSE,
-  bandwidth=.5,
-  nbins=NULL,
+  bandwidth = 0.5,
+  nbins = NULL,
   method = 'quasirandom',
-  groupOnX=NULL,
-  dodge.width=0,
+  groupOnX = NULL,
+  dodge.width = 0,
   ...,
   na.rm = FALSE,
   show.legend = NA,
   inherit.aes = TRUE,
-  raster.width=NULL, raster.height=NULL, raster.dpi=300
+  raster.width = NULL, raster.height = NULL, raster.dpi = 300
 ) {
 
-  if (!requireNamespace('ggbeeswarm', quietly = T)) {
-    stop('Install \"ggbeeswarm\" to use this function', call. = F)
-  }
-
   position <- ggbeeswarm::position_quasirandom(width = width, varwidth = varwidth, bandwidth = bandwidth, nbins = nbins,
                                                method = method, groupOnX = groupOnX, dodge.width = dodge.width)
 

R/geom-tile-rast.R

@@ -39,8 +39,12 @@ GeomTileRast <- ggplot2::ggproto(
 #' @param raster.width Width of the result image (in inches). Default: deterined by the current device parameters.
 #' @param raster.height Height of the result image (in inches). Default: deterined by the current device parameters.
 #' @param raster.dpi Resolution of the result image.
+#' @return geom_tile plot with rasterized layer
 #'
 #' @examples
+#' library(ggplot2)
+#' library(ggrastr)
+#'
 #' coords <- expand.grid(1:100, 1:100)
 #' coords$Value <- 1 / apply(as.matrix(coords), 1, function(x) sum((x - c(50, 50))^2)^0.01)
 #' ggplot(coords) + geom_tile_rast(aes(x=Var1, y=Var2, fill=Value))

R/utils.R

@@ -1,14 +1,20 @@
 #' Pretty theme
 #'
-#' @param show.ticks Show x- and y- ticks.
+#' @param show.ticks Show x- and y-ticks.
 #' @param legend.pos Vector with x and y position of the legend.
+#' @return ggplot2 with plot ticks and positioned legend
 #'
 #' @examples
-#' ggplot() + geom_point(aes(x=rnorm(1000), y=rnorm(1000), color=(1:1000 / 1000))) + theme_pdf(F, legend.pos=c(1, 1))
+#' library(ggplot2)
+#' library(ggrastr)
+#' 
+#' data = rnorm(100)
+#' colors = (1:100/100)
+#' ggplot() + geom_point(aes(x=data, y=data, color=colors)) + theme_pdf(FALSE, legend.pos=c(1, 1))
 #'
 #' @export
-theme_pdf <- function(show.ticks=T, legend.pos=NULL) {
-  r <- ggplot2::theme(axis.line = ggplot2::element_line(size=.7, color = "black"),
+theme_pdf <- function(show.ticks=TRUE, legend.pos=NULL) {
+  r <- ggplot2::theme(axis.line = ggplot2::element_line(size=0.7, color = "black"),
                       axis.text=ggplot2::element_text(size=12),
                       axis.title.x=ggplot2::element_text(margin=ggplot2::margin(t=3, unit='pt')),
                       axis.title.y=ggplot2::element_text(margin=ggplot2::margin(r=3, unit='pt')),
@@ -31,5 +37,6 @@ theme_pdf <- function(show.ticks=T, legend.pos=NULL) {
   if (!is.null(legend.pos)) {
     r <- r + ggplot2::theme(legend.position=legend.pos, legend.justification=legend.pos)
   }
+
   return(r)
 }