@@ -1,9 +1,55 @@

+##' Biplot of dimension-reduced data

+##'

+##' Visualize an overlay of a score plot and a loading plot using the

+##' [poplin_reduce] output.

+##'

+##' @param x A dimension-reduced data matrix produced by [poplin_reduce] or

+##'   \linkS4class{poplin} object containing dimension-reduced data.

+##' @param y A data matrix for loadings. Not required for the [reduce_pca] and

+##'   [reduce_plsda] outputs.

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

+##' @param comp A numeric vector of length 2 indicating two components to plot.

+##' @param group A discrete variable to visualize the grouping structure.

+##' @param group_col A vector of colors with the same length of unique values in

+##'   \code{group}.

+##' @param point_size The size of points.

+##' @param point_shape_by_group Logical controlling whether each group have

+##'   different shapes of data points. Also can be a numeric vector with the

+##'   same length of unique values in \code{group} to manually set point shapes.

+##' @param label Logical controlling whether score labels are shown instead of

+##'   points.

+##' @param label_subset A character vector specifying a subset of score labels

+##'   to display.

+##' @param ellipse Logical controlling whether data ellipses are shown using

+##'   [ggplot2::stat_ellipse].

+##' @param xlab The title of x-axis of the plot.

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

+##' @param title The main title of the plot.

+##' @param legend Logical controlling whether the plot legend is shown.

+##' @param arrow_len Numeric value controlling the length of arrow head.

+##' @param arrow_alpha Numeric value controlling the transparency of arrow.

+##' @param arrow_label Logical controlling whether text labels for arrows are

+##'   shown.

+##' @param arrow_label_ext Numeric value controlling the scalar extension for

+##'   arrow labels.

+##' @param arrow_label_size Numeric value controlling the size of arrow labels.

+##' @param arrow_label_col Character string indicating the color of arrow

+##'   labels.

+##' @param arrow_label_subset A character vector specifying a subset of arrow

+##'   labels to display.

+##' @param ... Arguments passed to the default method.

+##' @return A ggplot object.

+##' @seealso [poplin_reduce], [poplin_scoreplot].

+##' @name poplin_biplot

+NULL

+

 ##' @importFrom ggplot2 geom_segment scale_x_continuous scale_y_continuous sec_axis

 ##' @export

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

   UseMethod("poplin_biplot")

 }

+##' @rdname poplin_biplot

 ##' @export

 poplin_biplot.default <- function(x, y, comp = 1:2, group,

                                   group_col = NULL,

@@ -21,14 +67,14 @@ poplin_biplot.default <- function(x, y, comp = 1:2, group,

                                   arrow_label_col = "red",

                                   arrow_label_subset = NULL) {

   p <- poplin_scoreplot(x, comp = comp, group = group,

-                   group_col = group_col,

-                   point_shape_by_group = point_shape_by_group,

-                   point_size = point_size,

-                   label = label, label_size = label_size,

-                   label_subset = label_subset,

-                   ellipse = ellipse,

-                   xlab = xlab, ylab = ylab,

-                   title = title, legend = legend)

+                        group_col = group_col,

+                        point_shape_by_group = point_shape_by_group,

+                        point_size = point_size,

+                        label = label, label_size = label_size,

+                        label_subset = label_subset,

+                        ellipse = ellipse,

+                        xlab = xlab, ylab = ylab,

+                        title = title, legend = legend)

   scalers <- 0.7 * c(

     (max(x[, comp[1]]) - min(x[, comp[1]])) / (max(y[, comp[1]]) - min(y, comp[1])),

     (max(x[, comp[2]]) - min(x[, comp[2]])) / (max(y[, comp[2]]) - min(y, comp[2]))

@@ -63,6 +109,7 @@ poplin_biplot.default <- function(x, y, comp = 1:2, group,

   p

 }

+##' @rdname poplin_biplot

 ##' @export

 poplin_biplot.poplin.pca <- function(x, scale = 1, comp = 1:2, group, ...) {

   if (max(comp) > ncol(x) || length(comp) != 2) {

@@ -81,6 +128,7 @@ poplin_biplot.poplin.pca <- function(x, scale = 1, comp = 1:2, group, ...) {

   poplin_biplot.default(X, Y, comp = 1:2, group = group, ...)

 }

+##' @rdname poplin_biplot

 ##' @export

 poplin_biplot.poplin.plsda <- function(x, comp = 1:2,

                                        group = attr(x, "Y.observed"), ...) {

@@ -90,6 +138,7 @@ poplin_biplot.poplin.plsda <- function(x, comp = 1:2,

 }

+##' @rdname poplin_biplot

 ##' @export

 poplin_biplot.poplin <- function(x, poplin_in, comp = 1:2, ...) {

   if (!(poplin_in %in% poplin_reduced_names(x))) {

@@ -97,6 +146,13 @@ poplin_biplot.poplin <- function(x, poplin_in, comp = 1:2, ...) {

          "Input must be one of poplin_reduced_names(x).")

   }

   m <- poplin_reduced(x, poplin_in)

+  if (is.null(colnames(m))) {

+    stop("colnames of 'poplin_reduced(x, poplin_in)' must be non-NULL.")

+  }

+  if (label && is.null(rownames(m))) {

+    stop("rownames of 'poplin_reduced(x, poplin_in)' ",

+         "'must be non-NULL if label = TRUE.")

+  }

   poplin_biplot(m, comp = comp, ...)

   ## if (inherits(m, "poplin.pca")) {

   ##   poplin_biplot.poplin.pca(m, comp = comp, ...)

@@ -4,6 +4,7 @@

 ##'

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

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

+##' @param group A discrete variable to visualize the grouping structure.

 ##' @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.

@@ -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 gtable of aligned plots.

+##' @return gtable of aligned plots

 ##' @name poplin_naplot

 NULL

@@ -1,3 +1,36 @@

+##' Score plot of dimension-reduced data

+##'

+##' Visualize the data onto a lower-dimensional space using the [poplin_reduce]

+##' output.

+##'

+##' @param x A dimension-reduced data matrix produced by [poplin_reduce] or

+##'   \linkS4class{poplin} object containing dimension-reduced data.

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

+##' @param comp a numeric vector of length 2 indicating two components to plot.

+##' @param group A discrete variable to visualize the grouping structure.

+##' @param group_col A vector of colors with the same length of unique values in

+##'   \code{group}.

+##' @param point_size The size of points.

+##' @param point_shape_by_group Logical controlling whether each group have

+##'   different shapes of data points. Also can be a numeric vector with the

+##'   same length of unique values in \code{group} to manually set point shapes.

+##' @param label Logical controlling whether score labels are shown instead of

+##'   points.

+##' @param label_subset A character vector specifying a subset of score labels

+##'   to display.

+##' @param ellipse Logical controlling whether data ellipses are shown using

+##'   [ggplot2::stat_ellipse].

+##' @param xlab The title of x-axis of the plot.

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

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

+##' @param title The main title of the plot.

+##' @param legend Logical controlling whether the plot legend is shown.

+##' @param ... Arguments passed to the default method.

+##' @return A ggplot object.

+##' @seealso [poplin_reduce], [poplin_biplot].

+##' @name poplin_scoreplot

+NULL

+

 ##' @export

 ##' @importFrom ggplot2 ggplot aes geom_point geom_text stat_ellipse

 ##' @importFrom ggplot2 xlab ylab ggtitle theme_bw theme element_blank

@@ -6,6 +39,7 @@ poplin_scoreplot <- function(x, ...) {

   UseMethod("poplin_scoreplot")

 }

+##' @rdname poplin_scoreplot

 ##' @export

 poplin_scoreplot.default <- function(x, comp = c(1, 2), group,

                                 group_col = NULL,

@@ -93,6 +127,7 @@ poplin_scoreplot.default <- function(x, comp = c(1, 2), group,

   }

 }

+##' @rdname poplin_scoreplot

 ##' @export

 poplin_scoreplot.poplin.pca <- function(x, comp = c(1, 2),

                                         group, group_col = NULL,

@@ -127,6 +162,7 @@ poplin_scoreplot.poplin.pca <- function(x, comp = c(1, 2),

                            xlab = xlab, ylab = ylab, ...)

 }

+##' @rdname poplin_scoreplot

 ##' @export

 poplin_scoreplot.poplin.plsda <- function(x, comp = c(1, 2),

                                           group = attr(x, "Y.observed"),

@@ -160,6 +196,7 @@ poplin_scoreplot.poplin.plsda <- function(x, comp = c(1, 2),

                            xlab = xlab, ylab = ylab, ...)

 }

+##' @rdname poplin_scoreplot

 ##' @export

 poplin_scoreplot.poplin <- function(x, poplin_in, comp = 1:2, ...) {

   if (!(poplin_in %in% poplin_reduced_names(x))) {

@@ -167,5 +204,12 @@ poplin_scoreplot.poplin <- function(x, poplin_in, comp = 1:2, ...) {

          "Input must be one of poplin_reduced_names(x).")

   }

   m <- poplin_reduced(x, poplin_in)

+  if (is.null(colnames(m))) {

+    stop("colnames of 'poplin_reduced(x, poplin_in)' must be non-NULL.")

+  }

+  if (label && is.null(rownames(m))) {

+    stop("rownames of 'poplin_reduced(x, poplin_in)' ",

+         "'must be non-NULL if label = TRUE.")

+  } 

   poplin_scoreplot(m, comp = comp, ...)

 }

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

       stop("'", msg1, "' contains duplicates. ", msg2)

     }

     if (any(value_names %in% assay_names)) {

-      stop("'", msg1, "' must not overlap with assayNames(x). ", msg2)

+      stop("'", msg1, "' must not overlap with poplin_raw_names(x). ", msg2)

     }

   }

 }

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

   name_pool <- c(assayNames(x), poplin_data_names(x))

   if (!(name %in% name_pool)) {

     stop("data '", name, "' is not found in the poplin object.\n",

-         "Input must be one of c(assayNames(x), poplin_data_names(x).")

+         "Input must be one of c(poplin_raw_names(x), poplin_data_names(x).")

   }

   tryCatch(

     assay(x, name),

@@ -20,6 +20,8 @@

 \arguments{

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

+\item{group}{A discrete variable to visualize the grouping structure.}

+

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

 before plotting.}

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

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

 }

 \value{

-gtable of aligned plots.

+gtable of aligned plots

 }

 \description{

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

new file mode 100644

@@ -0,0 +1,93 @@

+% Generated by roxygen2: do not edit by hand

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

+\name{poplin_scoreplot}

+\alias{poplin_scoreplot}

+\alias{poplin_scoreplot.default}

+\alias{poplin_scoreplot.poplin.pca}

+\alias{poplin_scoreplot.poplin.plsda}

+\alias{poplin_scoreplot.poplin}

+\title{Score plot of dimension-reduced data}

+\usage{

+\method{poplin_scoreplot}{default}(

+  x,

+  comp = c(1, 2),

+  group,

+  group_col = NULL,

+  point_size = 1.5,

+  point_shape_by_group = FALSE,

+  label = FALSE,

+  label_size = 3.88,

+  label_subset = NULL,

+  ellipse = FALSE,

+  xlab = NULL,

+  ylab = NULL,

+  title = NULL,

+  legend = TRUE

+)

+

+\method{poplin_scoreplot}{poplin.pca}(

+  x,

+  comp = c(1, 2),

+  group,

+  group_col = NULL,

+  xlab = NULL,

+  ylab = NULL,

+  ...

+)

+

+\method{poplin_scoreplot}{poplin.plsda}(

+  x,

+  comp = c(1, 2),

+  group = attr(x, "Y.observed"),

+  group_col = NULL,

+  xlab = NULL,

+  ylab = NULL,

+  ...

+)

+

+\method{poplin_scoreplot}{poplin}(x, poplin_in, comp = 1:2, ...)

+}

+\arguments{

+\item{x}{A dimension-reduced data matrix produced by \link{poplin_reduce} or

+\linkS4class{poplin} object.}

+

+\item{comp}{a numeric vector of length 2 indicating two components to plot.}

+

+\item{group}{A discrete variable to visualize the grouping structure.}

+

+\item{group_col}{A vector of colors with the same length of unique values in

+\code{group}.}

+

+\item{point_size}{The size of points.}

+

+\item{point_shape_by_group}{Logical controlling whether each group have

+different shapes of data points. Also can be a numeric vector with the

+same length of unique values in \code{group} to manually set point shapes.}

+

+\item{label}{Logical controlling whether text labels are shown instead of

+points.}

+

+\item{label_subset}{A character vector to specify only a subset of text

+labels to display.}

+

+\item{ellipse}{Logical controlling whether data ellipses are shown using

+\link[ggplot2:stat_ellipse]{ggplot2::stat_ellipse}.}

+

+\item{xlab}{The title of x-axis of the plot.}

+

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

+

+\item{title}{The main title of the plot.}

+

+\item{legend}{Logical controlling whether the plot legend is shown.}

+

+\item{...}{Arguments passed to the default method.}

+

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

+}

+\value{

+A ggplot object.

+}

+\description{

+Visualize the data onto a lower-dimensional space.

+}