new file mode 100644

@@ -0,0 +1,24 @@

+##' FAAH knockout LC/MS data SummarizedExperiment

+##'

+##' A \linkS4class{SummarizedExperiment} object containing FAAH knockout LC/MS

+##' feature data from the \pkg{faahKO} (\code{faahko3} data) created with the

+##' \code{xcms::quantify} method.

+##'

+##' @references

+##'

+##' Colin A. Smith (2021). faahKO: Saghatelian et al. (2004) FAAH knockout LC/MS

+##' data. R package version 1.32.0. http://dx.doi.org/10.1021/bi0480335

+##'

+##' @examples

+##' faahko_se

+"faahko_se"

+

+##' FAAH knockout LC/MS data poplin

+##'

+##' A \linkS4class{poplin} object containing FAAH knockout LC/MS feature data

+##' from the \pkg{faahKO} (\code{faahko3} data) created by coercing the

+##' [faahko_se] object.

+##'

+##' @examples

+##' faahko_poplin

+"faahko_poplin"

@@ -21,7 +21,7 @@

 ##' @param method A imputation method. Default is 'pqn'.

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

 ##' @param poplin_out Name of a data matrix to store.

-##' @param ... Argument passed to a specific imputation method.

+##' @param ... Arguments passed to a specific imputation method.

 ##' @return A matrix or \linkS4class{poplin} object of the same dimension as

 ##'   \code{x} containing the imputed intensities.

 ##' @name poplin_impute

@@ -64,7 +64,7 @@ setMethod(

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

 ##' @param poplin_out Name of a data matrix to store.

 ##' @param by Imputation by k-nearest features or by k-nearest samples.

-##' @param ... Additional argument passed to [VIM::kNN].

+##' @param ... Additional arguments passed to [VIM::kNN].

 ##' @return A matrix or \linkS4class{poplin} object of the same dimension as

 ##'   \code{x} containing the imputed intensities.

 ##' @name impute_knn

@@ -106,7 +106,7 @@ setMethod(

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

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

 ##' @param poplin_out Name of a data matrix to store.

-##' @param ... Additional argument passed to [missForest::missForest].

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

 ##' @return A matrix or \linkS4class{poplin} object of the same dimension as

 ##'   \code{x} containing the imputed intensities.

 ##' @name impute_randomforest

@@ -148,7 +148,7 @@ setMethod(

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

 ##' @param poplin_out Name of a data matrix to store.

 ##' @param type A method for performing PCA.

-##' @param ... Additional argument passed to [pcaMethods::pca].

+##' @param ... Additional arguments passed to [pcaMethods::pca].

 ##' @return A matrix or \linkS4class{poplin} object of the same dimension as

 ##'   \code{x} containing the imputed intensities.

 ##' @name impute_pca

@@ -359,7 +359,7 @@ setMethod(

 ##' @param meanSdPlot If \code{TRUE}, the function shows [vsn::meanSdPlot] to

 ##'   visually verify whether there is a dependence of the standard deviation on

 ##'   the mean.

-##' @param ... Additional argument passed to [vsn::vsnMatrix].

+##' @param ... Additional arguments passed to [vsn::vsnMatrix].

 ##' @return A matrix or \linkS4class{poplin} object of the same dimension as

 ##'   \code{x} containing the normalized intensities.

 ##' @name normalize_vsn

@@ -1,8 +1,32 @@

+##' Missing value plot

+##'

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

+##' data matrix are recoded (1: missing; 0: non-missing) and visualized by

+##' rectangles.

+##'

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

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

+##' @param widths Relative widths of heatmap and dendrogram.

+##' @param height Relative height of heatmap and dendrogram.

+##' @param grid_gap Gap between cells.

+##' @param colors A vector of colors for heatmap.

+##' @param hide_colorbar Logical controlling whether the color bar (legend) is

+##'   hidden.

+##' @param showticklabels A logical vector of length 2 (x-axis, y-axis). If

+##'   \code{FALSE}, ticks are removed from the side of the plot.

+##' @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 gtable of aligned plot.

+##' @name poplin_naplot

+NULL

+

 ##' @export

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

   UseMethod("poplin_naplot")

 }

+##' @rdname poplin_naplot

 ##' @export

 ##' @importFrom heatmaply is.na10 heatmaply

 poplin_naplot.default <- function(x, widths = NULL, heights = NULL,

@@ -13,14 +37,25 @@ poplin_naplot.default <- function(x, widths = NULL, heights = NULL,

                  showticklabels = showticklabels,

                  row_dend_left = row_dend_left,

                  return_ppxpy = TRUE, plot_method = "ggplot", ...)

-  heatmaply:::arrange_plots(plots = p, hide_colorbar = hide_colorbar)

+  heatmaply:::arrange_plots(plots = p, widths = widths, heights = heights,

+                            hide_colorbar = hide_colorbar,

+                            row_dend_left = row_dend_left)

   ## temporary issue in arrange_plots in hide_colorbar

   ## .arrange_plots(plots = p, widths = widths, heights = heights,

   ##                hide_colorbar = hide_colorbar, row_dend_left = row_dend_left)

 }

+##' @rdname poplin_naplot

 ##' @export

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

+poplin_naplot.poplin <- function(x, poplin_in, widths = NULL, heights = NULL,

+                                 grid_gap = 1, color = viridis::viridis(2),

+                                 hide_colorbar = TRUE,

+                                 showticklabels = c(TRUE, FALSE),

+                                 row_dend_left = FALSE, ...) {

   m <- .verify_and_extract_input(x, poplin_in)

-  poplin_naplot.default(m, ...)

+  poplin_naplot.default(m, widths = widths, heigths = heights,

+                        grid_gap = grid_gap, color = color,

+                        hide_colorbar = hide_colorbar,

+                        showticklabels = showticklabels,

+                        row_dend_left = row_dend_left, ...)

 }

@@ -117,7 +117,7 @@ setMethod(

 ##' @param normalize if \code{TRUE}, an input matrix is mean-centered and scaled

 ##'   so that the largest absolute of the centered matrix is equal to unity. See

 ##'   [Rtsne::normalize_input] for details.

-##' @param ... Additional argument passed to [Rtsne::Rtsne].

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

 ##' @return A poplin.tsne matrix or \linkS4class{poplin} object with the same

 ##'   number of rows as \code{ncol(x)} containing the dimension reduction

 ##'   result.

@@ -161,7 +161,7 @@ setMethod(

 ##' @param ncomp Output dimensionality.

 ##' @param center A logical indicating mean-centering prior to PLS-DA.

 ##' @param scale A logical indicating unit variance scaling prior to PLS-DA.

-##' @param ... Additional argument passed to [pls::plsr].

+##' @param ... Additional arguments passed to [pls::plsr].

 ##' @return A poplin.plsda matrix or \linkS4class{poplin} object with the same

 ##'   number of rows as \code{ncol(x)} containing the dimension reduction

 ##'   result.

@@ -5,4 +5,5 @@ library(usethis)

 data(faahko3)

 faahko_se <- quantify(faahko3)

-use_data(faahko_se, overwrite = TRUE, version = 3)

+faahko_poplin <- as(faahko_se, "poplin")

+use_data(faahko_se, faahko_poplin, overwrite = TRUE, version = 3)

new file mode 100644

Binary files /dev/null and b/data/faahko_poplin.rda differ

new file mode 100644

@@ -0,0 +1,21 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/faahko_se.R

+\docType{data}

+\name{faahko_poplin}

+\alias{faahko_poplin}

+\title{FAAH knockout LC/MS data poplin}

+\format{

+An object of class \code{poplin} with 206 rows and 12 columns.

+}

+\usage{

+faahko_poplin

+}

+\description{

+A \linkS4class{poplin} object containing FAAH knockout LC/MS feature data

+from the \pkg{faahKO} (\code{faahko3} data) created by coercing the

+\link{faahko_se} object.

+}

+\examples{

+faahko_poplin

+}

+\keyword{datasets}

new file mode 100644

@@ -0,0 +1,25 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/faahko_se.R

+\docType{data}

+\name{faahko_se}

+\alias{faahko_se}

+\title{FAAH knockout LC/MS data SummarizedExperiment}

+\format{

+An object of class \code{SummarizedExperiment} with 206 rows and 12 columns.

+}

+\usage{

+faahko_se

+}

+\description{

+A \linkS4class{SummarizedExperiment} object containing FAAH knockout LC/MS

+feature data from the \pkg{faahKO} (\code{faahko3} data) created with the

+\code{xcms::quantify} method.

+}

+\examples{

+faahko_se

+}

+\references{

+Colin A. Smith (2021). faahKO: Saghatelian et al. (2004) FAAH knockout LC/MS

+data. R package version 1.32.0. http://dx.doi.org/10.1021/bi0480335

+}

+\keyword{datasets}

@@ -14,7 +14,7 @@

 \item{by}{Imputation by k-nearest features or by k-nearest samples.}

-\item{...}{Additional argument passed to \link[VIM:kNN]{VIM::kNN}.}

+\item{...}{Additional arguments passed to \link[VIM:kNN]{VIM::kNN}.}

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

@@ -20,7 +20,7 @@

 \item{type}{A method for performing PCA.}

-\item{...}{Additional argument passed to \link[pcaMethods:pca]{pcaMethods::pca}.}

+\item{...}{Additional arguments passed to \link[pcaMethods:pca]{pcaMethods::pca}.}

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

@@ -12,7 +12,7 @@

 \arguments{

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

-\item{...}{Additional argument passed to \link[missForest:missForest]{missForest::missForest}.}

+\item{...}{Additional arguments passed to \link[missForest:missForest]{missForest::missForest}.}

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

@@ -16,7 +16,7 @@

 visually verify whether there is a dependence of the standard deviation on

 the mean.}

-\item{...}{Additional argument passed to \link[vsn:vsn2]{vsn::vsnMatrix}.}

+\item{...}{Additional arguments passed to \link[vsn:vsn2]{vsn::vsnMatrix}.}

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

@@ -20,7 +20,7 @@

 \item{method}{A imputation method. Default is 'pqn'.}

-\item{...}{Argument passed to a specific imputation method.}

+\item{...}{Arguments passed to a specific imputation method.}

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

new file mode 100644

@@ -0,0 +1,65 @@

+% Generated by roxygen2: do not edit by hand

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

+\name{poplin_naplot}

+\alias{poplin_naplot}

+\alias{poplin_naplot.default}

+\alias{poplin_naplot.poplin}

+\title{Missing value plot}

+\usage{

+\method{poplin_naplot}{default}(

+  x,

+  widths = NULL,

+  heights = NULL,

+  grid_gap = 1,

+  colors = viridis::viridis(2),

+  hide_colorbar = TRUE,

+  showticklabels = c(TRUE, FALSE),

+  row_dend_left = FALSE,

+  ...

+)

+

+\method{poplin_naplot}{poplin}(

+  x,

+  poplin_in,

+  widths = NULL,

+  heights = NULL,

+  grid_gap = 1,

+  color = viridis::viridis(2),

+  hide_colorbar = TRUE,

+  showticklabels = c(TRUE, FALSE),

+  row_dend_left = FALSE,

+  ...

+)

+}

+\arguments{

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

+

+\item{widths}{Relative widths of heatmap and dendrogram.}

+

+\item{grid_gap}{Gap between cells.}

+

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

+

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

+hidden.}

+

+\item{showticklabels}{A logical vector of length 2 (x-axis, y-axis). If

+\code{FALSE}, ticks are removed from the side of the plot.}

+

+\item{row_dend_left}{Logical controlling whether the row dendrogram is

+placed on the left on the plot.}

+

+\item{...}{Additional arguments passed to \link[heatmaply:heatmaply]{heatmaply::heatmaply}.}

+

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

+

+\item{height}{Relative height of heatmap and dendrogram.}

+}

+\value{

+gtable of aligned plot.

+}

+\description{

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

+data matrix are recoded (1: missing; 0: non-missing) and visualized by

+rectangles.

+}

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

 \item{scale}{A logical indicating unit variance scaling prior to PLS-DA.}

-\item{...}{Additional argument passed to \link[pls:mvr]{pls::plsr}.}

+\item{...}{Additional arguments passed to \link[pls:mvr]{pls::plsr}.}

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

@@ -18,7 +18,7 @@

 so that the largest absolute of the centered matrix is equal to unity. See

 \link[Rtsne:normalize_input]{Rtsne::normalize_input} for details.}

-\item{...}{Additional argument passed to \link[Rtsne:Rtsne]{Rtsne::Rtsne}.}

+\item{...}{Additional arguments passed to \link[Rtsne:Rtsne]{Rtsne::Rtsne}.}

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