@@ -156,7 +156,6 @@ importFrom(ggplot2,theme)

 importFrom(ggplot2,theme_bw)

 importFrom(ggplot2,xlab)

 importFrom(ggplot2,ylab)

-importFrom(heatmaply,ggheatmap)

 importFrom(heatmaply,heatmaply)

 importFrom(heatmaply,is.na10)

 importFrom(methods,as)

@@ -1,15 +1,30 @@

+##' Box plot

+##'

+##' Produce a box-and-whisker plot of the feature intensity values.

+##'

+##' @param x A matrix or \linkS4class{poplin} object.

+##' @param poplin_in Name of a data matrix to retrieve.

+##' @param pre_log2 If \code{TRUE}, feature intensities are log2-transformed

+##'   before plotting.

+##' @param violin If \code{TRUE}, a violin plot is drawn instead of the boxplot.

+##' @param ylab The title of y-axis of the plot.

+##' @return A ggplot object.

+##' @name poplin_boxplot

+NULL

+

 ##' @export

 poplin_boxplot <- function(x, ...) {

   UseMethod("poplin_boxplot")

 }

+##' @rdname poplin_boxplot

 ##' @export

 ##' @importFrom stats reshape

 ##' @importFrom ggplot2 geom_boxplot geom_violin

-poplin_boxplot.default <- function(x, group, log2 = FALSE, violin = FALSE,

+poplin_boxplot.default <- function(x, group, pre_log2 = FALSE, violin = FALSE,

                            ylab = "Intensity") {

   ## convert wide to long format to draw fig

-  if (log2) {

+  if (pre_log2) {

     x <- log2(x)

   }

   dt <- as.data.frame(t(x))

@@ -38,8 +53,11 @@ poplin_boxplot.default <- function(x, group, log2 = FALSE, violin = FALSE,

           axis.title.x = element_blank())

 }

+##' @rdname poplin_boxplot

 ##' @export

-poplin_boxplot.poplin <- function(x, poplin_in, ...) {

+poplin_boxplot.poplin <- function(x, poplin_in, group, pre_log2 = FALSE,

+                                  violin = FALSE, ylab = "Intensity") {

   m <- .verify_and_extract_input(x, poplin_in)

-  poplin_boxplot.default(m, ...)

+  poplin_boxplot.default(m, group = group, pre_log2 = pre_log2,

+                         violin = violin, ylab = ylab)

 }

@@ -24,7 +24,7 @@

 ##' @param row_dend_left Logical controlling whether the row dendrogram is

 ##'   placed on the left on the plot.

 ##' @param ... Additional arguments passed to [heatmaply::heatmaply].

-##' @return \code{gtable} of aligned plots.

+##' @return gtable of aligned plots.

 ##' @name poplin_corplot

 NULL

@@ -36,7 +36,6 @@ poplin_corplot <- function(x, ...) {

 ##' @rdname poplin_corplot

 ##' @export

-##' @importFrom heatmaply ggheatmap

 poplin_corplot.default <- function(x, unit = c("sample", "feature"),

                      use = c("everything", "all.obs", "complete.obs",

                              "na.or.complete", "pairwise.complete.obs"),

@@ -19,7 +19,7 @@

 ##' @param row_dend_left Logical controlling whether the row dendrogram is

 ##'   placed on the left on the plot.

 ##' @param ... Additional arguments passed to [heatmaply::heatmaply].

-##' @return \code{gtable} of aligned plots.

+##' @return gtable of aligned plots.

 ##' @name poplin_naplot

 NULL

new file mode 100644

@@ -0,0 +1,37 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/plot-boxplot.R

+\name{poplin_boxplot}

+\alias{poplin_boxplot}

+\alias{poplin_boxplot.default}

+\alias{poplin_boxplot.poplin}

+\title{Box plot}

+\usage{

+\method{poplin_boxplot}{default}(x, group, pre_log2 = FALSE, violin = FALSE, ylab = "Intensity")

+

+\method{poplin_boxplot}{poplin}(

+  x,

+  poplin_in,

+  group,

+  pre_log2 = FALSE,

+  violin = FALSE,

+  ylab = "Intensity"

+)

+}

+\arguments{

+\item{x}{A matrix or \linkS4class{poplin} object.}

+

+\item{pre_log2}{If \code{TRUE}, feature intensities are log2-transformed

+before plotting.}

+

+\item{violin}{If \code{TRUE}, a violin plot is drawn instead of the boxplot.}

+

+\item{ylab}{The title of y-axis of the plot.}

+

+\item{poplin_in}{Name of a data matrix to retrieve.}

+}

+\value{

+A ggplot object.

+}

+\description{

+Produce a box-and-whisker plot of the feature intensity values.

+}

@@ -34,6 +34,8 @@

   widths = NULL,

   heights = NULL,

   colors = viridis::viridis(n = 256, alpha = 1, begin = 0, end = 1, option = "viridis"),

+  label = FALSE,

+  digits = 2,

   grid_gap = 0,

   hide_colorbar = FALSE,

   showticklabels = c(TRUE, TRUE),

@@ -59,7 +61,7 @@ to be computed. Refer to \code{?cor} for details.}

 \item{colors}{A vector of colors for heatmap.}

-\item{label}{If \code{TRUE}, cell values are shown.}

+\item{label}{Logical controlling whether cell values are shown.}

 \item{digits}{The desired number of digits when \code{label = TRUE}.}

@@ -79,7 +81,7 @@ placed on the left on the plot.}

 \item{poplin_in}{Name of a data matrix to retrieve.}

 }

 \value{

-\code{gtable} of aligned plots.

+gtable of aligned plots.

 }

 \description{

 Visualize correlations between samples or features. All values in a

@@ -11,6 +11,8 @@

   widths = NULL,

   heights = NULL,

   colors = viridis::viridis(2),

+  label = FALSE,

+  digits = 2,

   grid_gap = 1,

   hide_colorbar = TRUE,

   showticklabels = c(TRUE, FALSE),

@@ -23,7 +25,9 @@

   poplin_in,

   widths = NULL,

   heights = NULL,

-  color = viridis::viridis(2),

+  colors = viridis::viridis(2),

+  label = FALSE,

+  digits = 2,

   grid_gap = 1,

   hide_colorbar = TRUE,

   showticklabels = c(TRUE, FALSE),

@@ -40,6 +44,10 @@

 \item{colors}{A vector of colors for heatmap.}

+\item{label}{Logical controlling whether cell values are shown.}

+

+\item{digits}{The desired number of digits when \code{label = TRUE}.}

+

 \item{grid_gap}{Gap between cells.}

 \item{hide_colorbar}{Logical controlling whether the color bar (legend) is

@@ -56,7 +64,7 @@ placed on the left on the plot.}

 \item{poplin_in}{Name of a data matrix to retrieve.}

 }

 \value{

-\code{gtable} of aligned plots.

+gtable of aligned plots.

 }

 \description{

 Visualize data for exploring missing value (NA) patterns. All values in a