Add corplot

11 files changed, 741 insertions, 6 deletions

diff --git a/.Rbuildignore b/.Rbuildignore
new file mode 100644
index 0000000..5163d0b
--- /dev/null
+++ b/.Rbuildignore
@@ -0,0 +1 @@
+^LICENSE\.md$
diff --git a/DESCRIPTION b/DESCRIPTION
index f4837d1..8bc7286 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,10 +2,15 @@ Package: rcsobczak
 Title: Chris' R Namespace
 Version: 0.0.0.9000
 Authors@R: 
-    person("Chris", "Sobczak", , "chris@sobczak.family", role = c("aut", "cre"))
+    person("Chris", "Sobczak", , "chris@sobczak.family", role = c("aut", "cre"), comment = c(ORCID = "0009-0003-3398-2792"))
 Description: This is a collection of my personal functions.
-License: `use_mit_license()`, `use_gpl3_license()` or friends to pick a
-    license
+License: GPL-3 + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 8.0.0.9000
+Imports: 
+    ggplot2,
+    reshape2
+Suggests: 
+    testthat (>= 3.0.0)
+Config/testthat/edition: 3
diff --git a/LICENSE.md b/LICENSE.md
new file mode 100644
index 0000000..175443c
--- /dev/null
+++ b/LICENSE.md
@@ -0,0 +1,595 @@
+GNU General Public License
+==========================
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+
+IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY
+COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS THE PROGRAM AS
+PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL,
+INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE
+PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE
+OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE
+WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGES.
+
+### 17. Interpretation of Sections 15 and 16
+
+If the disclaimer of warranty and limitation of liability provided above cannot be
+given local legal effect according to their terms, reviewing courts shall apply local
+law that most closely approximates an absolute waiver of all civil liability in
+connection with the Program, unless a warranty or assumption of liability accompanies
+a copy of the Program in return for a fee.
+
+_END OF TERMS AND CONDITIONS_
+
+## How to Apply These Terms to Your New Programs
+
+If you develop a new program, and you want it to be of the greatest possible use to
+the public, the best way to achieve this is to make it free software which everyone
+can redistribute and change under these terms.
+
+To do so, attach the following notices to the program. It is safest to attach them
+to the start of each source file to most effectively state the exclusion of warranty;
+and each file should have at least the “copyright” line and a pointer to
+where the full notice is found.
+
+    <one line to give the program's name and a brief idea of what it does.>
+    Copyright (C) <year>  <name of author>
+
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+If the program does terminal interaction, make it output a short notice like this
+when it starts in an interactive mode:
+
+    <program>  Copyright (C) <year>  <name of author>
+    This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'.
+    This is free software, and you are welcome to redistribute it
+    under certain conditions; type 'show c' for details.
+
+The hypothetical commands `show w` and `show c` should show the appropriate parts of
+the General Public License. Of course, your program's commands might be different;
+for a GUI interface, you would use an “about box”.
+
+You should also get your employer (if you work as a programmer) or school, if any, to
+sign a “copyright disclaimer” for the program, if necessary. For more
+information on this, and how to apply and follow the GNU GPL, see
+&lt;<http://www.gnu.org/licenses/>&gt;.
+
+The GNU General Public License does not permit incorporating your program into
+proprietary programs. If your program is a subroutine library, you may consider it
+more useful to permit linking proprietary applications with the library. If this is
+what you want to do, use the GNU Lesser General Public License instead of this
+License. But first, please read
+&lt;<http://www.gnu.org/philosophy/why-not-lgpl.html>&gt;.
diff --git a/NAMESPACE b/NAMESPACE
index 6e2a175..713d046 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,3 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+export(corplot)
 export(gg_csobczak)
+import(ggplot2)
+importFrom(reshape2,melt)
diff --git a/R/corplot.R b/R/corplot.R
new file mode 100644
index 0000000..c18e904
--- /dev/null
+++ b/R/corplot.R
@@ -0,0 +1,79 @@
+utils::globalVariables(c('i', 'j', 'value'))
+#' Correlation PLot (Upper Triangle)
+#'
+#' Minimal ggplot2 correlation plot showing the upper triangle
+#' in the top-right corner with no axis labels.
+#' @param R A square numeric correlation matrix
+#' @param title Optional plot title
+#'
+#' @return A ggplot object
+#'
+#' @examples
+#' X <- matrix(data = rnorm(100), nrow = 10)
+#' R <- cor(X)
+#' corplot(R, title = 'Example Correlation Plot')
+#'
+#' @importFrom reshape2 melt
+#' @import ggplot2
+#' @export
+corplot <- function(R, title = NULL){
+	R <- tryCatch({
+		if(is.matrix(R)){
+			if(nrow(R) == ncol(R)){
+				R[upper.tri(R)]
+			}
+		}else if(is.vector(R)){
+			m <- length(R)
+			n <- (1 + sqrt(1 + 8 * m)) / 2
+			if(n == floor(n)){
+				R
+			}else{
+				stop('Input length not compatible with upper triangle')
+			}
+		}else{
+			Rm <- as.matrix(R)
+			if(nrow(Rm) == ncol(Rm)){
+				Rm[upper.tri(Rm)]
+			}
+		}
+	}, error = function(e){
+		stop(paste('Invalid input for corplot:', e$message))
+	})
+
+	# Now get a df from the upper triangle
+	m <- length(R)
+	n <- as.integer((1 + sqrt(1 + 8 * m)) / 2)
+	M <- matrix(NA, n, n)
+	M[upper.tri(M)] <- R
+	df <- reshape2::melt(M, na.rm = TRUE)
+	colnames(df) <- c('i', 'j', 'value')
+	df$i <- factor(df$i, levels = 1:n)
+	df$j <- factor(df$j, levels = 1:n)
+
+	# And plot it
+	p <- ggplot2::ggplot(
+		data = df,
+		ggplot2::aes(x = i, y = j, fill = value)
+	) +
+	ggplot2::geom_tile() +
+	ggplot2::scale_fill_gradient2(
+		low = 'red',
+		mid = 'white',
+		high = 'blue',
+		midpoint = 0,
+		name = expression(rho)
+	) +
+	ggplot2::scale_x_discrete(limits = rev(levels(df$i))) +
+	ggplot2::scale_y_discrete(limits = levels(df$j)) +
+	ggplot2::coord_fixed() +
+	ggplot2::theme_void()
+
+	if(!is.null(title)){
+		p <- p +
+		ggplot2::ggtitle(title) +
+		ggplot2::theme(
+			plot.title = ggplot2::element_text(hjust = 0.5)
+		)
+	}
+	return(p)
+}
diff --git a/R/gg_csobczak.R b/R/gg_csobczak.R
index 97448a3..2817637 100644
--- a/R/gg_csobczak.R
+++ b/R/gg_csobczak.R
@@ -4,10 +4,12 @@
 #' @param p A ggplot object to add formatting to.
 #' @keywords ggplot plot p
 #' @export
+#' @import ggplot2
 #' @examples
 #' df <- data.frame(x=rnorm(10), y=rnorm(10))
-#' p <- ggplot(data=df, aes(x=x, y=y)) + geom_point()
+#' p <- ggplot2::ggplot(data=df, ggplot2::aes(x = x, y = y)) + ggplot2::geom_point()
 #' p <- gg_csobczak(p)
 gg_csobczak <- function(p){
-	p + theme_classic()
+	p <- p + ggplot2::theme_classic()
+	return(p)
 }
diff --git a/man/corplot.Rd b/man/corplot.Rd
new file mode 100644
index 0000000..72d4df0
--- /dev/null
+++ b/man/corplot.Rd
@@ -0,0 +1,26 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/corplot.R
+\name{corplot}
+\alias{corplot}
+\title{Correlation PLot (Upper Triangle)}
+\usage{
+corplot(R, title = NULL)
+}
+\arguments{
+\item{R}{A square numeric correlation matrix}
+
+\item{title}{Optional plot title}
+}
+\value{
+A ggplot object
+}
+\description{
+Minimal ggplot2 correlation plot showing the upper triangle
+in the top-right corner with no axis labels.
+}
+\examples{
+X <- matrix(data = rnorm(100), nrow = 10)
+R <- cor(X)
+corplot(R, title = 'Example Correlation Plot')
+
+}
diff --git a/man/gg_csobczak.Rd b/man/gg_csobczak.Rd
index d5951a1..70495d5 100644
--- a/man/gg_csobczak.Rd
+++ b/man/gg_csobczak.Rd
@@ -14,7 +14,7 @@ This adds standard formating to my ggplots.
 }
 \examples{
 df <- data.frame(x=rnorm(10), y=rnorm(10))
-p <- ggplot(data=df, aes(x=x, y=y)) + geom_point()
+p <- ggplot2::ggplot(data=df, ggplot2::aes(x = x, y = y)) + ggplot2::geom_point()
 p <- gg_csobczak(p)
 }
 \keyword{ggplot}
diff --git a/tests/testthat.R b/tests/testthat.R
new file mode 100644
index 0000000..c015e8f
--- /dev/null
+++ b/tests/testthat.R
@@ -0,0 +1,12 @@
+# This file is part of the standard setup for testthat.
+# It is recommended that you do not modify it.
+#
+# Where should you do additional test configuration?
+# Learn more about the roles of various files in:
+# * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
+# * https://testthat.r-lib.org/articles/special-files.html
+
+library(testthat)
+library(rcsobczak)
+
+test_check("rcsobczak")
diff --git a/tests/testthat/test-corplot.R b/tests/testthat/test-corplot.R
new file mode 100644
index 0000000..2aecdc1
--- /dev/null
+++ b/tests/testthat/test-corplot.R
@@ -0,0 +1,5 @@
+test_that("returns a ggplot object", {
+	x <- matrix(data = rnorm(100), nrow = 10)
+	p <- corplot(x)
+	inherits(p, 'ggplot')
+})
diff --git a/tests/testthat/test-gg_csobczak.R b/tests/testthat/test-gg_csobczak.R
new file mode 100644
index 0000000..ca99bef
--- /dev/null
+++ b/tests/testthat/test-gg_csobczak.R
@@ -0,0 +1,7 @@
+test_that("returns a ggplot object", {
+	df <- data.frame(x = rnorm(10), y = rnorm(10))
+	p <- ggplot2::ggplot(data = df, ggplot2::aes(x = x, y = y)) +
+	ggplot2::geom_point()
+	p <- gg_csobczak(p)
+	inherits(p, 'ggplot')
+})