Merge pull request #21 from ToxPi/dev

Issue-19: Changing maintainer

DESCRIPTION

@@ -3,8 +3,12 @@ Type: Package
 Title: Create ToxPi Prioritization Models
 Version: 1.3.0
 Authors@R: 
-    c(person("Dayne L", "Filer", 
-             role = c("aut", "cre", "fnd"), 
+    c(person("Jonathon F", "Fleming",
+             role = c("aut","cre"),
+             email = "jffleming0129@gmail.com",
+             comment = c(ORCID = "0000-0003-2447-3139")),
+      person("Dayne L", "Filer", 
+             role = c("aut", "fnd"), 
              email = "dayne.filer@gmail.com",
              comment = c(ORCID = "0000-0002-3443-5315")),
       person("Dillon T", "Lloyd",
@@ -14,8 +18,6 @@ Authors@R:
              comment = c(ORCID = "0000-0001-5447-0129")),
       person("Skylar W", "Marvel",
              role = "aut"),
-      person("Jonathon", "Fleming",
-             role = "aut"),
       person("Alison A", "Motsinger-Reif",
              role = c("fnd"),
              comment = c(ORCID = "0000-0003-1346-2493")),

NEWS.md

@@ -1,3 +1,12 @@
+# toxpiR 1.3.0
+
+* Added 'txpMissing' slot to TxpResult; this stores information regarding the 
+  amount of missing data in the dataset per slice
+* Added ggplot capabilities for plotting with several new aesthetics
+* Updated vignettes
+* Transferred maintainer to Jonathon F Fleming
+
+
 # toxpiR 1.2.0
 
 * Now require R>=4.0 due to reports of installation issues

README.md

@@ -2,11 +2,11 @@
 
 <!-- badges: start -->
   [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
-  [![R-CMD-check](https://github.com/ToxPi/toxpiR/workflows/R-CMD-check/badge.svg)](https://github.com/ToxPi/toxpiR/actions)
+  [![R-CMD-check](https://github.com/ToxPi/toxpiR/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/ToxPi/toxpiR/actions/workflows/R-CMD-check.yaml)
   [![cran-version](https://www.r-pkg.org/badges/version-last-release/toxpiR?color=blue)](https://cran.r-project.org/web/packages/toxpiR/index.html)
   [![downloads](https://cranlogs.r-pkg.org/badges/grand-total/toxpiR)](https://cranlogs.r-pkg.org/badges/grand-total/toxpiR)
   [![codecov](https://codecov.io/gh/ToxPi/toxpiR/branch/main/graph/badge.svg?token=7yocvT0KzZ)](https://codecov.io/gh/ToxPi/toxpiR)
-[![R-CMD-check](https://github.com/ToxPi/toxpiR/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/ToxPi/toxpiR/actions/workflows/R-CMD-check.yaml)
+
 <!-- badges: end -->
 
 R package for the Toxicological Priority Index (ToxPi) prioritization algorithm. 

tests/testthat/test-TxpResult.R

@@ -62,7 +62,7 @@ test_that("TxpResult accessors return expected slots", {
   expect_equal(txpValueNames(res), txpValueNames(txpSlices(txpModel(res))))
   expect_equal(txpValueNames(res, simplify = TRUE), 
                txpValueNames(txpSlices(txpModel(res)), simplify = TRUE))
-  expect_is(txpMissing(res), "numeric")
+  expect_type(txpMissing(res), "double")
   expect_equal(length(txpMissing(res)), length(txpSlices(res)))
   expect_true(all(txpMissing(res) >=0 & txpMissing(res) <=1))
   expect_equal(txpMissing(res), c(s1 = 0.1,s2 =0.1,s3 =0.125,s4 =0.1))
@@ -159,7 +159,7 @@ test_that("TxpResult show method displays correct information", {
 ##----------------------------------------------------------------------------##
 ## Plot -- TxpResult, missing
 
-test_that("We can make ToxPi diagrams", {
+test_that("We can make and edit ToxPi diagrams", {
   expect_silent({
     data(txp_example_input, package = "toxpiR")
     data(txp_example_model, package = "toxpiR")
@@ -168,15 +168,18 @@ test_that("We can make ToxPi diagrams", {
                               id.var = "name")
   })
   expect_silent(plot(res))
+  expect_silent(grid.edit("pie-1", fills = NULL))
+  grid.edit("pie-10::slice1", gp = gpar(fill = "#7DBC3D"))
   expect_silent(plot(res, package = "gg"))
   expect_silent(plot(res, package = "gg",fills = c("red","blue","green","magenta")))
   expect_silent(plot(res, package = "gg",showScore = FALSE))
   expect_silent(plot(res, package = "gg",ncol = 2))
   expect_silent(plot(res, package = "gg",bgcolor = "white"))
-  expect_silent(plot(res, package = "gg",sliceBorderColor = "#FF00FF"))
+  expect_silent(plot(res, package = "gg",sliceBorderColor = NULL))
   expect_silent(plot(res, package = "gg",sliceValueColor = "#FF00FF",))
   expect_silent(plot(res, package = "gg",sliceLineColor = "#FF00FF"))
   expect_silent(plot(res, package = "gg",showMissing = FALSE))
+  expect_silent(plot(res, package = "gg",showCenter = FALSE))
 })
 
 ##----------------------------------------------------------------------------##

vignettes/introduction.Rmd

@@ -42,7 +42,7 @@ knitr::opts_chunk$set(
 
 ## Introduction
 
-This document introduces ToxPi and describes how to use the `toxpiR` package to easily import, recombine, analyze, and visualize high dimensional data. The `toxpiR` package is an R implementation of ToxPi that offers new features over what was previously available for data handling, recombination, and customization; provides formally packaged, open-source code for ToxPi; extends the application domain by supporting rapid analysis of massive datasets; and bridges with the stand-alone, [Graphical User Interface (GUI)](https://toxpi.org) Java application and [ArcGIS Toolkit](https://github.com/Jonathon-Fleming/ToxPi-GIS). 
+This document introduces ToxPi and describes how to use the `toxpiR` package to easily import, recombine, analyze, and visualize high dimensional data. The `toxpiR` package is an R implementation of ToxPi that offers new features over what was previously available for data handling, recombination, and customization; provides formally packaged, open-source code for ToxPi; extends the application domain by supporting rapid analysis of massive datasets; and bridges with the stand-alone, [Graphical User Interface (GUI)](https://toxpi.org) Java application and [ArcGIS Toolkit](https://github.com/ToxPi/ToxPi-GIS). 
 
 ## What is ToxPi?