Merge pull request #83 from jasenfinch/devel

v0.14.6

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: metabolyseR
 Title: Methods for Pre-Treatment, Data Mining and Correlation Analyses of Metabolomics Data
-Version: 0.14.5
+Version: 0.14.6
 Authors@R: person("Jasen", "Finch", email = "jsf9@aber.ac.uk", role = c("aut", "cre"))
 Description: A tool kit for pre-treatment, modelling, feature selection and correlation analyses of metabolomics data.
 URL: https://jasenfinch.github.io/metabolyseR

NEWS.md

@@ -1,3 +1,9 @@
+# metabolyseR 0.14.6
+
+* [`plotExplanatoryHeatmap`](https://jasenfinch.github.io/metabolyseR/reference/plotExplanatoryHeatmap.html) method for the [`Analysis`](https://jasenfinch.github.io/metabolyseR/reference/Analysis-class.html) class now returns the plot only if the number of plots is equal to 1. 
+
+* Removed reference to the `nCores` parameter from the documentation example of [`metabolyse()`](https://jasenfinch.github.io/metabolyseR/reference/metabolyse.html).
+
 # metabolyseR 0.14.5
 
 * Correlation analysis results now include an absolute correlation coefficient column by which the results are also arranged in descending order.

R/metabolyse.R

@@ -28,9 +28,8 @@
 #' )
 #' parameters(p,'modelling') <- modellingParameters('anova')
 #' 
-#' ## Change "cls" and "nCores" parameters 
+#' ## Change "cls" parameters 
 #' changeParameter(p,'cls') <- 'day'
-#' changeParameter(p,'nCores') <- 2
 #' 
 #' ## Run analysis using a subset of the abr1 negative mode data set
 #' analysis <- metabolyse(abr1$neg[,1:200],

R/plotExplanatoryHeatmap.R

@@ -493,12 +493,18 @@ setMethod('plotExplanatoryHeatmap',
                    clusterMethod = 'ward.D2', 
                    featureNames = TRUE,
                    featureLimit = Inf){
-            x %>%
+            pl <- x %>%
               analysisResults(element = 'modelling') %>%
               plotExplanatoryHeatmap(threshold = threshold, 
                                      distanceMeasure = distanceMeasure, 
                                      clusterMethod = clusterMethod, 
                                      featureNames = featureNames,
-                                     featureLimit = featureLimit) 
+                                     featureLimit = featureLimit)
+
+            if (length(pl) == 1){
+              pl <- pl[[1]]
+            }
+
+            return(pl)
           }
 )

README.Rmd

@@ -15,7 +15,7 @@ knitr::opts_chunk$set(collapse = TRUE,
 # metabolyseR
 
 <!-- badges: start -->
-[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
+[![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
 [![R-CMD-check](https://github.com/jasenfinch/metabolyseR/workflows/R-CMD-check/badge.svg)](https://github.com/jasenfinch/metabolyseR/actions)
 [![codecov](https://codecov.io/gh/jasenfinch/metabolyseR/branch/master/graph/badge.svg)](https://codecov.io/gh/jasenfinch/metabolyseR/branch/master) 
 [![license](https://img.shields.io/badge/license-GNU%20GPL%20v3.0-blue.svg)](https://github.com/jasenfinch/metabolyseR/blob/master/DESCRIPTION)

README.md

@@ -6,7 +6,7 @@
 <!-- badges: start -->
 
 [![Lifecycle:
-experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
+stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
 [![R-CMD-check](https://github.com/jasenfinch/metabolyseR/workflows/R-CMD-check/badge.svg)](https://github.com/jasenfinch/metabolyseR/actions)
 [![codecov](https://codecov.io/gh/jasenfinch/metabolyseR/branch/master/graph/badge.svg)](https://codecov.io/gh/jasenfinch/metabolyseR/branch/master)
 [![license](https://img.shields.io/badge/license-GNU%20GPL%20v3.0-blue.svg)](https://github.com/jasenfinch/metabolyseR/blob/master/DESCRIPTION)