@@ -1,7 +1,8 @@

 Package: Glimma

 Type: Package

 Title: Interactive HTML graphics

-Version: 1.15.1

+Version: 1.13.2

+Date: 2016-12-21

 Authors@R: 

     c(

         person(

@@ -54,7 +55,7 @@ Suggests:

 License: GPL-3 | file LICENSE

 URL: https://github.com/Shians/Glimma

 BugReports: https://github.com/Shians/Glimma/issues

-RoxygenNote: 6.1.1

+RoxygenNote: 7.1.0

 NeedsCompilation: no

 LazyData: true

 VignetteBuilder: knitr

@@ -68,7 +68,7 @@ hasRows <- function(...) {

 isType <- function(x, typename, typecheck=NULL) {

     if (is.null(typecheck)) {

         typecheck <- function(x) {

-            output <- class(x) == typename

+            output <- is(x, typename)

             output

         }

@@ -31,7 +31,7 @@ checkObjAnnoCountsShapes <- function(anno, counts, x) {

 # check that side.main exists as a column in either anno or main object

 checkSideMainPresent <- function(side.main, anno, x) {

-    if (class(x) == "DGELRT" || class(x) == "DGEExact") {

+    if (is(x, "DGELRT") || is(x, "DGEExact")) {

         if (side.main %!in% union(colnames(anno), colnames(x$table))) {

             stop(paste("column", quotify(side.main), "cannot be found in x$table or anno."))

         }

@@ -40,7 +40,7 @@ checkSideMainPresent <- function(side.main, anno, x) {

         } else {

             combined_anno <- anno

         }

-    } else if (class(x) == "MArrayLM") {

+    } else if (is(x, "MArrayLM")) {

         if (side.main %!in% union(colnames(anno), colnames(x$genes))) {

             stop(paste("column", quotify(side.main), "cannot be found in x$genes or anno."))

         }

@@ -49,7 +49,7 @@ checkSideMainPresent <- function(side.main, anno, x) {

         } else {

             combined_anno <- anno

         }

-    } else if (class(x) == "DESeqResults") {

+    } else if (is(x, "DESeqResults")) {

         if (side.main %!in% union(colnames(anno), names(x@listData))) {

             stop(paste("column", quotify(side.main), "cannot be found in x or anno."))

         }

@@ -68,4 +68,4 @@ checkSideMainPresent <- function(side.main, anno, x) {

             combined_anno <- anno

         }

     }

-}

\ No newline at end of file

+}

@@ -29,7 +29,7 @@

 #' des <- model.matrix(~genotype)

 #'

 #' ## Apply voom with sample quality weights and fit linear model

-#' v <- voomWithQualityWeights(x, design=des, normalize.method="none", plot=FALSE)

+#' v <- voomWithQualityWeights(x, design=des, plot=FALSE)

 #' vfit <- lmFit(v,des)

 #'

 #' ## Apply treat relative to a fold-change of 1.5

@@ -57,7 +57,6 @@ glMDPlot <- function(x, ...) {

 #'

 #' @author Shian Su

 #'

-#' @inheritParams glMDPlot

 #' @param x the data.frame object containing expression and fold change values.

 #' @param xval the column to plot on x axis of left plot.

 #' @param yval the column to plot on y axis of left plot.

@@ -185,7 +184,6 @@ glMDPlot.default <- function(

 #'

 #' @author Shian Su

 #'

-#' @inheritParams glMDPlot

 #' @param x the DGELRT object.

 #' @param counts the matrix of expression values, with samples in columns.

 #' @param anno the data.frame containing gene annotations.

@@ -368,7 +366,7 @@ glMDPlot.DGEExact <- glMDPlot.DGELRT

 #' des <- model.matrix(~genotype)

 #'

 #' ## Apply voom with sample quality weights and fit linear model

-#' v <- voomWithQualityWeights(x, design=des, normalize.method="none", plot=FALSE)

+#' v <- voomWithQualityWeights(x, design=des, plot=FALSE)

 #' vfit <- lmFit(v,des)

 #'

 #' ## Apply treat relative to a fold-change of 1.5

@@ -118,7 +118,7 @@ glMDSPlot.default <- function(

     # Method for MDS objects

     points <- a1$points

-    if (!is.data.frame(groups) && class(groups) != "DataFrame") {

+    if (!is.data.frame(groups) && !is(groups, "DataFrame")) {

     # Rename for the column name in dataframe

         groups <- data.frame(groups)

     }

@@ -203,7 +203,7 @@ glMDSPlot.DGEList <- function (

     labels = NULL,

     groups = rep(1, ncol(x)),

     gene.selection = c("pairwise", "common"),

-    prior.count = 0.25,

+    prior.count = 2,

     main = "MDS Plot",

     path = getwd(),

     folder = "glimma-plots",

@@ -292,16 +292,16 @@ glMDSPlot.DESeqDataSet <- function(

 # extract sample groups based on object class

 getLabels <- function(x, labels) {

-    

+

     if (is.null(labels)) {

-        if (class(x) == "DGEList") {

-            # DGElist get from 

+        if (is(x, "DGEList")) {

+            # DGElist get from

             if (not.null(x$samples$groups)) {

                 labels <- rownames(x$samples)

             } else {

                 labels <- seq_cols(x)

             }

-        } else if (class(x) == "DESeqDataSet") {

+        } else if (is(x, "DESeqDataSet")) {

             # DESeqDaset

             if (not.null(SummarizedExperiment::colData(x))) {

                 labels <- rownames(SummarizedExperiment::colData(x))

@@ -28,7 +28,7 @@ glimma <- function(..., layout=c(1, 1), path=getwd(), folder="glimma-plots",

     ##

     # Input checking

     for (i in list(...)) {

-        if (class(i) == "jschart") {

+        if (is(i, "jschart")) {

             nplots <- nplots + 1

         }

     }

@@ -82,7 +82,7 @@ glimma <- function(..., layout=c(1, 1), path=getwd(), folder="glimma-plots",

     )

     cat(

-        temp, 

+        temp,

         file = file.path(path, folder, paste0(html, ".html")),

         sep = "\n"

     )

@@ -1,13 +1,15 @@

-Changes IN Glimma 1.15.1

-  * Updated unit test for new default colour palette in R 4.0.0

+Changes in Glimma 1.9.4

-Changes IN Glimma 1.6.0

+  * Fixed tests for R4.0.0

+  * Fixed examples for limma voom (normlization argument is now normalize.method)

+

+Changes in Glimma 1.6.0

   * Added table to MDS plot.

   * Changed encoding of javascript data to be more compact

   * Fixed handling of top and gene.selection parameters in glMDSPlot

-CHANGES IN Glimma 1.3.0

+Changes in Glimma 1.3.0

   * Added highlighting to bars in MDS plot.

   * Added interaction with table when clicking on points in MD plot.

@@ -16,7 +18,7 @@ CHANGES IN Glimma 1.3.0

   * Changed style of table.

   * Changed size of highlighted points.

-CHANGES IN Glimma 1.2.0

+Changes in Glimma 1.2.0

   * Added option to turn off internal cpm transform (transform=FALSE) in MD Plot.

   * Added gridlines to MD Plot.

@@ -31,27 +33,27 @@ CHANGES IN Glimma 1.2.0

   * Fixed logical values in annotation breaking graphs.

   * Fixed numeric values not working for colours.

-CHANGES IN Glimma 1.1.0

+Changes in Glimma 1.1.0

   * Added tables to MD Plot.

-CHANGES IN Glimma 1.0.0

+Changes in Glimma 1.0.0

   * Bioconductor release version.

-CHANGES IN Glimma 0.99.4:

+Changes in Glimma 0.99.4:

   * Added sample colours for MD plot.

   * Added DESeqResults method for glMDPlot

-CHANGES IN Glimma 0.99.3:

+Changes in Glimma 0.99.3:

   * Imported p.adjust for relevant functions.

-CHANGES IN Glimma 0.99.2:

+Changes in Glimma 0.99.2:

   * Added don't test cases for non-exported functions to pass checks.

-CHANGES IN Glimma 0.99.1:

+Changes in Glimma 0.99.1:

   * Initial package creation.

@@ -4,10 +4,23 @@

 \alias{glBar.default}

 \title{Glimma MD Plot}

 \usage{

-\method{glBar}{default}(x, yval, names.arg = rownames(x),

-  ndigits = NULL, signif = 6, xlab = NULL, ylab = yval,

-  main = NULL, height = 400, width = 500, colval = NULL,

-  annot = yval, flag = NULL, info = NULL, ...)

+\method{glBar}{default}(

+  x,

+  yval,

+  names.arg = rownames(x),

+  ndigits = NULL,

+  signif = 6,

+  xlab = NULL,

+  ylab = yval,

+  main = NULL,

+  height = 400,

+  width = 500,

+  colval = NULL,

+  annot = yval,

+  flag = NULL,

+  info = NULL,

+  ...

+)

 }

 \arguments{

 \item{x}{the data.frame containing data to plot.}

@@ -4,15 +4,32 @@

 \alias{glMDPlot.DESeqDataSet}

 \title{Glimma MD Plot}

 \usage{

-\method{glMDPlot}{DESeqDataSet}(x, counts = NULL, anno, groups,

-  samples = NULL, status = rep(0, nrow(x)), transform = FALSE,

-  main = "", xlab = "Mean Expression", ylab = "log-fold-change",

-  side.xlab = "Group", side.ylab = "logMean", side.log = FALSE,

+\method{glMDPlot}{DESeqDataSet}(

+  x,

+  counts = NULL,

+  anno,

+  groups,

+  samples = NULL,

+  status = rep(0, nrow(x)),

+  transform = FALSE,

+  main = "",

+  xlab = "Mean Expression",

+  ylab = "log-fold-change",

+  side.xlab = "Group",

+  side.ylab = "logMean",

+  side.log = FALSE,

   side.gridstep = ifelse(!transform || side.log, FALSE, 0.5),

-  jitter = 30, side.main = "GeneID", display.columns = NULL,

+  jitter = 30,

+  side.main = "GeneID",

+  display.columns = NULL,

   cols = c("#00bfff", "#858585", "#ff3030"),

-  sample.cols = rep("#1f77b4", ncol(x)), path = getwd(),

-  folder = "glimma-plots", html = "MD-Plot", launch = TRUE, ...)

+  sample.cols = rep("#1f77b4", ncol(x)),

+  path = getwd(),

+  folder = "glimma-plots",

+  html = "MD-Plot",

+  launch = TRUE,

+  ...

+)

 }

 \arguments{

 \item{x}{the DESeqDataSet object.}

@@ -4,15 +4,32 @@

 \alias{glMDPlot.DESeqResults}

 \title{Glimma MD Plot}

 \usage{

-\method{glMDPlot}{DESeqResults}(x, counts = NULL, anno, groups,

-  samples = NULL, status = rep(0, nrow(x)), transform = FALSE,

-  main = "", xlab = "Mean Expression", ylab = "log-fold-change",

-  side.xlab = "Group", side.ylab = "Expression", side.log = FALSE,

+\method{glMDPlot}{DESeqResults}(

+  x,

+  counts = NULL,

+  anno,

+  groups,

+  samples = NULL,

+  status = rep(0, nrow(x)),

+  transform = FALSE,

+  main = "",

+  xlab = "Mean Expression",

+  ylab = "log-fold-change",

+  side.xlab = "Group",

+  side.ylab = "Expression",

+  side.log = FALSE,

   side.gridstep = ifelse(!transform || side.log, FALSE, 0.5),

-  jitter = 30, side.main = "GeneID", display.columns = NULL,

+  jitter = 30,

+  side.main = "GeneID",

+  display.columns = NULL,

   cols = c("#00bfff", "#858585", "#ff3030"),

-  sample.cols = rep("#1f77b4", ncol(counts)), path = getwd(),

-  folder = "glimma-plots", html = "MD-Plot", launch = TRUE, ...)

+  sample.cols = rep("#1f77b4", ncol(counts)),

+  path = getwd(),

+  folder = "glimma-plots",

+  html = "MD-Plot",

+  launch = TRUE,

+  ...

+)

 }

 \arguments{

 \item{x}{the DESeqResults object.}

@@ -4,16 +4,33 @@

 \alias{glMDPlot.DGEExact}

 \title{Glimma MD Plot}

 \usage{

-\method{glMDPlot}{DGEExact}(x, counts = NULL, anno = NULL,

-  groups = NULL, samples = NULL, status = rep(0, nrow(x)),

-  transform = FALSE, main = "", xlab = "Average log CPM",

-  ylab = "log-fold-change", side.xlab = "Group",

-  side.ylab = "Expression", side.log = FALSE,

+\method{glMDPlot}{DGEExact}(

+  x,

+  counts = NULL,

+  anno = NULL,

+  groups = NULL,

+  samples = NULL,

+  status = rep(0, nrow(x)),

+  transform = FALSE,

+  main = "",

+  xlab = "Average log CPM",

+  ylab = "log-fold-change",

+  side.xlab = "Group",

+  side.ylab = "Expression",

+  side.log = FALSE,

   side.gridstep = ifelse(!transform || side.log, FALSE, 0.5),

-  p.adj.method = "BH", jitter = 30, side.main = "GeneID",

-  display.columns = NULL, cols = c("#00bfff", "#858585", "#ff3030"),

-  sample.cols = rep("#1f77b4", ncol(counts)), path = getwd(),

-  folder = "glimma-plots", html = "MD-Plot", launch = TRUE, ...)

+  p.adj.method = "BH",

+  jitter = 30,

+  side.main = "GeneID",

+  display.columns = NULL,

+  cols = c("#00bfff", "#858585", "#ff3030"),

+  sample.cols = rep("#1f77b4", ncol(counts)),

+  path = getwd(),

+  folder = "glimma-plots",

+  html = "MD-Plot",

+  launch = TRUE,

+  ...

+)

 }

 \arguments{

 \item{x}{the DGEExact object.}

@@ -4,16 +4,33 @@

 \alias{glMDPlot.DGELRT}

 \title{Glimma MD Plot}

 \usage{

-\method{glMDPlot}{DGELRT}(x, counts = NULL, anno = NULL,

-  groups = NULL, samples = NULL, status = rep(0, nrow(x)),

-  transform = FALSE, main = "", xlab = "Average log CPM",

-  ylab = "log-fold-change", side.xlab = "Group",

-  side.ylab = "Expression", side.log = FALSE,

+\method{glMDPlot}{DGELRT}(

+  x,

+  counts = NULL,

+  anno = NULL,

+  groups = NULL,

+  samples = NULL,

+  status = rep(0, nrow(x)),

+  transform = FALSE,

+  main = "",

+  xlab = "Average log CPM",

+  ylab = "log-fold-change",

+  side.xlab = "Group",

+  side.ylab = "Expression",

+  side.log = FALSE,

   side.gridstep = ifelse(!transform || side.log, FALSE, 0.5),

-  p.adj.method = "BH", jitter = 30, side.main = "GeneID",

-  display.columns = NULL, cols = c("#00bfff", "#858585", "#ff3030"),

-  sample.cols = rep("#1f77b4", ncol(counts)), path = getwd(),

-  folder = "glimma-plots", html = "MD-Plot", launch = TRUE, ...)

+  p.adj.method = "BH",

+  jitter = 30,

+  side.main = "GeneID",

+  display.columns = NULL,

+  cols = c("#00bfff", "#858585", "#ff3030"),

+  sample.cols = rep("#1f77b4", ncol(counts)),

+  path = getwd(),

+  folder = "glimma-plots",

+  html = "MD-Plot",

+  launch = TRUE,

+  ...

+)

 }

 \arguments{

 \item{x}{the DGELRT object.}

@@ -4,16 +4,34 @@

 \alias{glMDPlot.MArrayLM}

 \title{Glimma MD Plot}

 \usage{

-\method{glMDPlot}{MArrayLM}(x, counts = NULL, anno = NULL,

-  groups = NULL, samples = NULL, status = rep(0, nrow(x)),

-  transform = FALSE, main = "", xlab = "Average log CPM",

-  ylab = "log-fold-change", side.main = "GeneID",

-  side.xlab = "Group", side.ylab = "Expression", side.log = FALSE,

+\method{glMDPlot}{MArrayLM}(

+  x,

+  counts = NULL,

+  anno = NULL,

+  groups = NULL,

+  samples = NULL,

+  status = rep(0, nrow(x)),

+  transform = FALSE,

+  main = "",

+  xlab = "Average log CPM",

+  ylab = "log-fold-change",

+  side.main = "GeneID",

+  side.xlab = "Group",

+  side.ylab = "Expression",

+  side.log = FALSE,

   side.gridstep = ifelse(!transform || side.log, FALSE, 0.5),

-  coef = ncol(x$coefficients), p.adj.method = "BH", jitter = 30,

-  display.columns = NULL, cols = c("#00bfff", "#858585", "#ff3030"),

-  sample.cols = rep("#1f77b4", ncol(counts)), path = getwd(),

-  folder = "glimma-plots", html = "MD-Plot", launch = TRUE, ...)

+  coef = ncol(x$coefficients),

+  p.adj.method = "BH",

+  jitter = 30,

+  display.columns = NULL,

+  cols = c("#00bfff", "#858585", "#ff3030"),

+  sample.cols = rep("#1f77b4", ncol(counts)),

+  path = getwd(),

+  folder = "glimma-plots",

+  html = "MD-Plot",

+  launch = TRUE,

+  ...

+)

 }

 \arguments{

 \item{x}{the MArrayLM object.}

@@ -103,7 +121,7 @@ x <- calcNormFactors(x, method="TMM")

 des <- model.matrix(~genotype)

 ## Apply voom with sample quality weights and fit linear model

-v <- voomWithQualityWeights(x, design=des, normalize.method="none", plot=FALSE)

+v <- voomWithQualityWeights(x, design=des, plot=FALSE)

 vfit <- lmFit(v,des)

 ## Apply treat relative to a fold-change of 1.5

@@ -38,7 +38,7 @@ x <- calcNormFactors(x, method="TMM")

 des <- model.matrix(~genotype)

 ## Apply voom with sample quality weights and fit linear model

-v <- voomWithQualityWeights(x, design=des, normalize.method="none", plot=FALSE)

+v <- voomWithQualityWeights(x, design=des, plot=FALSE)

 vfit <- lmFit(v,des)

 ## Apply treat relative to a fold-change of 1.5

@@ -4,16 +4,34 @@

 \alias{glMDPlot.default}

 \title{Glimma MD Plot}

 \usage{

-\method{glMDPlot}{default}(x, xval, yval, counts = NULL, anno = NULL,

-  groups = NULL, samples = NULL, status = rep(0, nrow(x)),

-  transform = FALSE, main = "", xlab = xval, ylab = yval,

-  side.main = "GeneID", side.xlab = "Group",

-  side.ylab = "Expression", side.log = FALSE,

+\method{glMDPlot}{default}(

+  x,

+  xval,

+  yval,

+  counts = NULL,

+  anno = NULL,

+  groups = NULL,

+  samples = NULL,

+  status = rep(0, nrow(x)),

+  transform = FALSE,

+  main = "",

+  xlab = xval,

+  ylab = yval,

+  side.main = "GeneID",

+  side.xlab = "Group",

+  side.ylab = "Expression",

+  side.log = FALSE,

   side.gridstep = ifelse(!transform || side.log, FALSE, 0.5),

-  jitter = 30, display.columns = side.main, cols = c("#00bfff",

-  "#858585", "#ff3030"), sample.cols = rep("#1f77b4", ncol(counts)),

-  path = getwd(), folder = "glimma-plots", html = "MD-Plot",

-  launch = TRUE, ...)

+  jitter = 30,

+  display.columns = side.main,

+  cols = c("#00bfff", "#858585", "#ff3030"),

+  sample.cols = rep("#1f77b4", ncol(counts)),

+  path = getwd(),

+  folder = "glimma-plots",

+  html = "MD-Plot",

+  launch = TRUE,

+  ...

+)

 }

 \arguments{

 \item{x}{the data.frame object containing expression and fold change values.}

@@ -4,10 +4,20 @@

 \alias{glMDSPlot.DESeqDataSet}

 \title{Glimma MDS Plot}

 \usage{

-\method{glMDSPlot}{DESeqDataSet}(x, top = 500, labels = NULL,

-  groups = NULL, gene.selection = c("pairwise", "common"),

-  prior.count = 0.25, main = "MDS Plot", path = getwd(),

-  folder = "glimma-plots", html = "MDS-Plot", launch = TRUE, ...)

+\method{glMDSPlot}{DESeqDataSet}(

+  x,

+  top = 500,

+  labels = NULL,

+  groups = NULL,

+  gene.selection = c("pairwise", "common"),

+  prior.count = 0.25,

+  main = "MDS Plot",

+  path = getwd(),

+  folder = "glimma-plots",

+  html = "MDS-Plot",

+  launch = TRUE,

+  ...

+)

 }

 \arguments{

 \item{x}{the DESeqDataSet containing the gene expressions.}

@@ -4,10 +4,20 @@

 \alias{glMDSPlot.DGEList}

 \title{Glimma MDS Plot}

 \usage{

-\method{glMDSPlot}{DGEList}(x, top = 500, labels = NULL,

-  groups = rep(1, ncol(x)), gene.selection = c("pairwise", "common"),

-  prior.count = 0.25, main = "MDS Plot", path = getwd(),

-  folder = "glimma-plots", html = "MDS-Plot", launch = TRUE, ...)

+\method{glMDSPlot}{DGEList}(

+  x,

+  top = 500,

+  labels = NULL,

+  groups = rep(1, ncol(x)),

+  gene.selection = c("pairwise", "common"),

+  prior.count = 2,

+  main = "MDS Plot",

+  path = getwd(),

+  folder = "glimma-plots",

+  html = "MDS-Plot",

+  launch = TRUE,

+  ...

+)

 }

 \arguments{

 \item{x}{the DGEList containing the gene expressions.}

@@ -4,10 +4,19 @@

 \alias{glMDSPlot.default}

 \title{Glimma MDS Plot}

 \usage{

-\method{glMDSPlot}{default}(x, top = 500, labels = seq_cols(x),

-  groups = rep(1, ncol(x)), gene.selection = c("pairwise", "common"),

-  main = "MDS Plot", path = getwd(), folder = "glimma-plots",

-  html = "MDS-Plot", launch = TRUE, ...)

+\method{glMDSPlot}{default}(

+  x,

+  top = 500,

+  labels = seq_cols(x),

+  groups = rep(1, ncol(x)),

+  gene.selection = c("pairwise", "common"),

+  main = "MDS Plot",

+  path = getwd(),

+  folder = "glimma-plots",

+  html = "MDS-Plot",

+  launch = TRUE,

+  ...

+)

 }

 \arguments{

 \item{x}{the matrix containing the gene expressions.}

@@ -4,13 +4,35 @@

 \alias{glScatter.default}

 \title{Glimma Scatter Plot}

 \usage{

-\method{glScatter}{default}(x, xval = "x", yval = "y", idval = NULL,

-  point.size = 2, x.jitter = 0, y.jitter = 0, ndigits = NULL,

-  signif = 6, log = "", xgrid = FALSE, ygrid = FALSE,

-  xstep = FALSE, ystep = FALSE, xlab = xval, ylab = yval,

-  main = NULL, height = 400, width = 500, colval = NULL,

-  annot = c(xval, yval), annot.lab = NULL, flag = NULL,

-  info = NULL, hide = FALSE, disable = NULL, ...)

+\method{glScatter}{default}(

+  x,

+  xval = "x",

+  yval = "y",

+  idval = NULL,

+  point.size = 2,

+  x.jitter = 0,

+  y.jitter = 0,

+  ndigits = NULL,

+  signif = 6,

+  log = "",

+  xgrid = FALSE,

+  ygrid = FALSE,

+  xstep = FALSE,

+  ystep = FALSE,

+  xlab = xval,

+  ylab = yval,

+  main = NULL,

+  height = 400,

+  width = 500,

+  colval = NULL,

+  annot = c(xval, yval),

+  annot.lab = NULL,

+  flag = NULL,

+  info = NULL,

+  hide = FALSE,

+  disable = NULL,

+  ...

+)

 }

 \arguments{

 \item{x}{the data.frame containing data to plot.}

@@ -4,13 +4,29 @@

 \alias{glXYPlot}

 \title{Glimma XY Plot}

 \usage{

-glXYPlot(x, y, counts = NULL, groups = NULL, samples = NULL,

-  status = rep(0, nrow(data)), anno = NULL, display.columns = NULL,

-  xlab = "x", ylab = "y", side.main = "GeneID",

-  side.xlab = "Group", side.ylab = "Expression",

-  sample.cols = rep("#1f77b4", length(groups)), cols = c("#00bfff",

-  "#858585", "#ff3030"), jitter = 30, path = getwd(),

-  folder = "glimma-plots", html = "XY-Plot", launch = TRUE, ...)

+glXYPlot(

+  x,

+  y,

+  counts = NULL,

+  groups = NULL,

+  samples = NULL,

+  status = rep(0, nrow(data)),

+  anno = NULL,

+  display.columns = NULL,

+  xlab = "x",

+  ylab = "y",

+  side.main = "GeneID",

+  side.xlab = "Group",

+  side.ylab = "Expression",

+  sample.cols = rep("#1f77b4", length(groups)),

+  cols = c("#00bfff", "#858585", "#ff3030"),

+  jitter = 30,

+  path = getwd(),

+  folder = "glimma-plots",

+  html = "XY-Plot",

+  launch = TRUE,

+  ...

+)

 }

 \arguments{

 \item{x}{a numeric vector of values to plot on the x-axis of the summary plot.}

@@ -4,9 +4,15 @@

 \alias{glimma}

 \title{Glimma plot manager}

 \usage{

-glimma(..., layout = c(1, 1), path = getwd(),

-  folder = "glimma-plots", html = "index", overwrite = TRUE,

-  launch = TRUE)

+glimma(

+  ...,

+  layout = c(1, 1),

+  path = getwd(),

+  folder = "glimma-plots",

+  html = "index",

+  overwrite = TRUE,

+  launch = TRUE

+)

 }

 \arguments{

 \item{...}{the jschart or jslink objects for processing.}

@@ -4,8 +4,15 @@

 \alias{gllink}

 \title{Plot linkages}

 \usage{

-gllink(from, to, src = "none", dest = "none", flag = "none",

-  both = FALSE, info = "none")

+gllink(

+  from,

+  to,

+  src = "none",

+  dest = "none",

+  flag = "none",

+  both = FALSE,

+  info = "none"

+)

 }

 \arguments{

 \item{from}{the index of the plot from which the event is dispatched.}

@@ -4,8 +4,7 @@

 \alias{makeJson.data.frame}

 \title{JSON converter for data frames}

 \usage{

-\method{makeJson}{data.frame}(df, convert.logical = TRUE,

-  dataframe = c("rows", "columns"))

+\method{makeJson}{data.frame}(df, convert.logical = TRUE, dataframe = c("rows", "columns"))

 }

 \arguments{

 \item{df}{the data.frame to be converted into JSON}

@@ -17,12 +17,10 @@ test_that("hex colour tools are correct", {

     expect_warning(as.hexcol(0))

     expect_equal(as.hexcol(1), "#000000")

-    # R changed default palette in 4.0.0

-    Rver <- with(R.Version(), paste(major, minor, sep = "."))

-    post_4.0 <- compareVersion(Rver, "4.0.0") >= 0

-    if (post_4.0) {

-        expect_equal(as.hexcol(2), "#df536b")

-    } else {

+    # R4.0.0 changed palette

+    if (getRversion() < "4.0.0") {

         expect_equal(as.hexcol(2), "#ff0000")

+    } else {

+        expect_equal(as.hexcol(2), "#df536b")

     }

 })