WIP: unify param def (#140)

Signed-off-by: Daena Rys <[email protected]>

R/getNeatOrder.R

@@ -23,9 +23,9 @@
 #' entities being analyzed (e.g. features or samples). There should be 2 columns
 #' only representing 2 PCs.
 #' 
-#' @param centering A single \code{character} value specifying the method to
+#' @param centering \code{Character scalar}. Specifies the method to
 #' center the data. Options are \code{"mean"}, \code{"median"}, or \code{NULL}
-#' if your data is already centered. (default: \code{"mean"})
+#' if your data is already centered. (Default: \code{"mean"})
 #' 
 #' @param ... Additional arguments passed to other methods.
 #'

R/plotAbundance.R

@@ -13,59 +13,56 @@
 #'   \code{\link[SummarizedExperiment:SummarizedExperiment-class]{SummarizedExperiment}}
 #'   object.
 #'
-#' @param rank a single \code{character} value defining the taxonomic rank to
-#'   use. Must be a value of \code{taxonomyRanks(x)}.
+#' @param rank \code{Character scalar}. Defines the taxonomic rank to
+#'   use. Must be a value of \code{taxonomyRanks(x)}. (Default: \code{NULL})
 #'
-#' @param assay.type a \code{character} value defining which assay data to
-#'   use. (default: \code{assay.type = "relabundance"})
+#' @param assay.type \code{Character scalar} value defining which assay data to
+#'   use. (Default: \code{"relabundance"})
 #'   
-#' @param assay_name a single \code{character} value for specifying which
-#'   assay to use for calculation.
-#'   (Please use \code{assay.type} instead. At some point \code{assay_name}
-#'   will be disabled.)
+#' @param assay_name Deprecate. Use \code{assay.type} instead.
 #'   
-#' @param col.var a single \code{character} value defining a column from 
+#' @param col.var \code{Character scalar}. Selects a column from 
 #'   \code{colData} to be plotted below the abundance plot.
 #'   Continuous numeric values will be plotted as point, whereas factors and
-#'   character will be plotted as colour-code bar. (default: \code{col.var =
-#'   NULL})
+#'   character will be plotted as colour-code bar. (Default: \code{NULL})
 #'   
 #' @param features Deprecated. Use \code{col.var} instead.
 #'   
-#' @param order.row.by How to order abundance value: By name (\dQuote{name}) 
+#' @param order.row.by \code{Character scalar}. How to order abundance value: By name (\dQuote{name}) 
 #' for sorting the taxonomic labels alphabetically, by abundance (\dQuote{abund}) to
 #' sort by abundance values or by a reverse order of abundance values (\dQuote{revabund}).
 #' 
 #' @param order_rank_by Deprecated. Use \code{order.row.by} instead.  
 #'   
-#' @param order.col.by A single character value from the chosen rank of abundance
+#' @param order.col.by \code{Character scalar}. from the chosen rank of abundance
 #'   data or from \code{colData} to select values to order the abundance
-#'   plot by. (default: \code{order.col.by = NULL})
+#'   plot by. (Default: \code{NULL})
 #'   
 #' @param order_sample_by Deprecated. Use \code{order.col.by} instead.
 #'   
-#' @param decreasing TRUE or FALSE: If the \code{order.col.by} is defined and the
+#' @param decreasing \code{Logical scalar}. If the \code{order.col.by} is defined and the
 #'   values are numeric, should the values used to order in decreasing or
-#'   increasing fashion? (default: \code{decreasing = FALSE})
+#'   increasing fashion? (Default: \code{FALSE})
 #'
-#' @param layout Either \dQuote{bar} or \dQuote{point}. 
+#' @param layout \code{Character scalar}. Either \dQuote{bar} or \dQuote{point}. 
 #' 
-#' @param one.facet Should the plot be returned in on facet or split into 
+#' @param one.facet \code{Logical scalar}. Should the plot be returned in on facet or split into 
 #'   different facet, one facet per different value detect in \code{rank}. If
 #'   \code{col.var} or \code{order.col.by} is not \code{NULL}, this setting will
-#'   be disregarded.
+#'   be disregarded. (Default: \code{TRUE})
 #'   
 #' @param one_facet Deprecated. Use \code{one.facet} instead.
 #' 
-#' @param ncol,scales if \code{one.facet = FALSE}, \code{ncol} defines many 
-#'   columns should be for plotting the different facets and \code{scales} is
-#'   used to define the behavior of the scales of each facet. Both values are 
-#'   passed onto \code{\link[ggplot2:facet_wrap]{facet_wrap}}.
+#' @param ncol \code{Numeric scalar}. if \code{one.facet = FALSE}, \code{ncol} defines many 
+#'   columns should be for plotting the different facets. (Default: \code{2})
+#'   
+#' @param scales \code{Character scalar}. Defines the behavior of the scales of each facet. Both values are 
+#'   passed onto \code{\link[ggplot2:facet_wrap]{facet_wrap}}. (Default: \code{"fixed"})
 #' 
 #' @param ... additional parameters for plotting.
 #'   \itemize{
-#'   \item{as.relative}{ \code{TRUE} or \code{FALSE}: Should the relative values
-#'   be calculated? (default: \code{as.relative = FALSE} }
+#'   \item \code{as.relative} \code{Character scalar}. Should the relative values
+#'   be calculated? (Default: \code{FALSE})
 #' }
 #' See \code{\link{mia-plot-args}} for more details i.e. call \code{help("mia-plot-args")}
 #'

R/plotAbundanceDensity.R

@@ -1,48 +1,37 @@
 #' Plot abundance density
 #'
 #' This function plots abundance of the most abundant taxa. 
-#'
-#' @param x a
-#'   \code{\link[SummarizedExperiment:SummarizedExperiment-class]{SummarizedExperiment}}
-#'   object.
 #' 
-#' @param layout a single character value for selecting the layout of the plot.
+#' @inheritParams plotAbundance
+#'
+#' @param layout \code{Character scalar}. Selects the layout of the plot.
 #'   There are three different options: \code{jitter}, \code{density}, and
 #'   \code{point} plot. (default: \code{layout = "jitter"})
-#'
-#' @param assay.type a single character value for selecting the
-#'   \code{\link[SummarizedExperiment:SummarizedExperiment-class]{assay}} to be
-#'   plotted. (default: \code{assay.type = "counts"})
-#'
-#' @param assay_name a single \code{character} value for specifying which
-#'   assay to use for calculation.
-#'   (Please use \code{assay.type} instead. At some point \code{assay_name}
-#'   will be disabled.)
 #'   
-#' @param n a positive integer specifying the number of the most abundant taxa
-#'   to show. (default: \code{n = min(nrow(x), 25L)})
+#' @param n \code{Integer scalar}. Specifies the number of the most abundant taxa
+#'   to show. (Default: \code{min(nrow(x), 25L)})
 #'  
-#' @param colour.by a single character value defining a column from
+#' @param colour.by \code{Character scalar}. Defines a column from
 #'   \code{colData}, that is used to color plot. Must be a value of
-#'   \code{colData()} function. (default: \code{colour.by = NULL})
+#'   \code{colData()} function. (Default: \code{NULL})
 #'   
 #' @param colour_by Deprecated. Use \code{colour.by} instead.
 #' 
-#' @param shape.by a single character value defining a column from
+#' @param shape.by \code{Character scalar}. Defines a column from
 #'   \code{colData}, that is used to group observations to different point shape
 #'   groups. Must be a value of \code{colData()} function. \code{shape.by} is
-#'   disabled when \code{layout = "density"}. (default: \code{shape.by = NULL})
+#'   disabled when \code{layout = "density"}. (Default: \code{NULL})
 #'   
 #' @param shape_by Deprecated. Use \code{shape.by} instead.
 #' 
-#' @param size.by a single character value defining a column from
+#' @param size.by \code{Character scalar}. Defines a column from
 #'   \code{colData}, that is used to group observations to different point size
 #'   groups. Must be a value of \code{colData()} function. \code{size.by} is
-#'   disabled when \code{layout = "density"}. (default: \code{size.by = NULL})
+#'   disabled when \code{layout = "density"}. (Default: \code{NULL})
 #'   
 #' @param size_by Deprecated. Use \code{size.by} instead.
 #' 
-#' @param decreasing \code{Boolean} indicating whether the results should be ordered 
+#' @param decreasing \code{Logical scalar}. Indicates whether the results should be ordered 
 #'   in a descending order or not. If \code{NA} is given the order
 #'   as found in \code{x} for the \code{n} most abundant taxa is used.
 #'   (Default: \code{TRUE})
@@ -51,31 +40,30 @@
 #'   
 #' @param ... additional parameters for plotting. 
 #' \itemize{
-#'   \item{xlab}{ a single character value for selecting the x-axis label. 
-#'   (default: \code{xlab = assay.type}) }
+#'   \item \code{xlab} \code{Character scalar}. Selects the x-axis label. 
+#'   (Default: \code{assay.type})
 #'   
-#'   \item{ylab}{ a single character value for selecting the y-axis label. 
+#'   \item \code{ylab} \code{Character scalar}. Selects the y-axis label. 
 #'   \code{ylab} is disabled when \code{layout = "density"}. 
-#'   (default: \code{ylab = "Taxa")} }
+#'   (Default: \code{"Taxa"})
 #'   
-#'   \item{point_alpha}{ a numeric value from range 0 to 1 selecting the transparency of
-#'   colour in \code{jitter} and \code{point} plot. (default: \code{point_alpha = 0.6}) }
+#'   \item \code{point.alpha} \code{Numeric scalar}. From range 0 to 1. Selects the transparency of
+#'   colour in \code{jitter} and \code{point} plot. (Default: \code{0.6})
 #'   
-#'   \item{point_shape}{ a positive integer value selecting the shape of point in
-#'   \code{jitter} and \code{point} plot. (default: \code{point_shape = 21}) }
+#'   \item \code{point.shape} \code{Positive integer scalar}. Value selecting the shape of point in
+#'   \code{jitter} and \code{point} plot. (Default: \code{21})
 #'   
-#'   \item{point_size}{ a positive numeric value selecting the size of point in
-#'   \code{jitter} and \code{point} plot. (default: \code{point_size = 2}) }
+#'   \item \code{point.size} \code{Positive integer scalar}. Selects the size of point in
+#'   \code{jitter} and \code{point} plot. (Default: \code{2})
 #'   
-#'   \item{add_legend}{ a boolean value selecting if legend is added. 
-#'   (default: \code{add_legend = TRUE}) }
+#'   \item \code{add_legend} \code{Logical scalar}. Determines if legend is added. 
+#'   (Default: \code{TRUE})
 #'   
-#'   \item{flipped}{ a boolean value selecting if the orientation of plot is changed 
-#'   so that x-axis and y-axis are swapped. (default \code{flipped = FALSE}) }
+#'   \item \code{flipped}: \code{Logical scalar}. Determines if the orientation of plot is changed 
+#'   so that x-axis and y-axis are swapped. (Default: \code{FALSE})
 #'   
-#'   \item{add_x_text}{ a boolean value selecting if text that represents values is included
-#'   in x-axis. (default: \code{add_x_text = TRUE}) }
-#'
+#'   \item \code{add_x_text} \code{Logical scalar}. Determines if text that represents values is included
+#'   in x-axis. (Default: \code{TRUE})
 #' }
 #' See \code{\link{mia-plot-args}} for more details i.e. call \code{help("mia-plot-args")}
 #'
@@ -122,14 +110,14 @@
 #' # Point shape is changed from default (21) to 41.
 #' plotAbundanceDensity(
 #'     tse, layout = "point", assay.type = "relabundance", n = 10,
-#'     point_shape = 41)
+#'     point.shape = 41)
 #'                      
 #' # Plots the relative abundance of 10 most abundant taxa as a point plot.
 #' # In addition to colour, groups can be visualized by size and shape in point plots,
 #' # and adjusted for point size
 #' plotAbundanceDensity(
 #'     tse, layout = "point", assay.type = "relabundance", n = 10,
-#'     shape.by = "Geographical_location", size.by = "Age", point_size=1)
+#'     shape.by = "Geographical_location", size.by = "Age", point.size=1)
 #' 
 #' # Ordering via decreasing
 #' plotAbundanceDensity(

R/plotCCA.R

@@ -8,71 +8,71 @@
 #'   \code{\link[TreeSummarizedExperiment:TreeSummarizedExperiment-constructor]{TreeSummarizedExperiment}}
 #'   or a matrix of weights. The latter is returned as output from \code{\link[mia:runCCA]{getRDA}}.
 #' 
-#' @param dimred A string or integer scalar indicating the reduced dimension to
+#' @param dimred \code{Character scalar} or \code{integer scalar}. Determines the reduced dimension to
 #'   plot. This is the output of \code{\link[mia:runCCA]{addRDA}} and resides in
 #'   \code{reducedDim(tse, dimred)}.
 #' 
 #' @param add.ellipse One of \code{c(TRUE, FALSE, "fill", "colour", "color")},
 #'   indicating whether ellipses should be present, absent, filled or colored.
 #'   (default: \code{ellipse.fill = TRUE})
 #'
-#' @param ellipse.alpha Number between 0 and 1 to adjust the opacity of ellipses.
-#'   (default: \code{ellipse.alpha = 0.2})
+#' @param ellipse.alpha \code{Numeric scalar}. Between 0 and 1. Adjusts the opacity of ellipses.
+#'   (Default: \code{0.2})
 #'
-#' @param ellipse.linewidth Number specifying the size of ellipses.
-#'   (default: \code{ellipse.linewidth = 0.1})
+#' @param ellipse.linewidth \code{Numeric scalar}. Specifies the size of ellipses.
+#'   (Default: \code{0.1})
 #' 
-#' @param ellipse.linetype Discrete number specifying the style of ellipses.
-#'   (default: \code{ellipse.linetype = 1})
+#' @param ellipse.linetype \code{Integer scalar}. Specifies the style of ellipses.
+#'   (Default: \code{1})
 #'   
-#' @param confidence.level Number between 0 and 1 to adjust confidence level.
-#'   (default: \code{confidence.level = 0.95})
+#' @param confidence.level \code{Numeric scalar}. Between 0 and 1. Adjusts confidence level.
+#'   (Default: \code{0.95})
 #'
-#' @param add.vectors TRUE or FALSE, should vectors appear in the plot.
-#'    (default: \code{add.vectors = TRUE})
+#' @param add.vectors \code{Logical scalar}. Should vectors appear in the plot.
+#'    (Default: \code{TRUE})
 #' 
-#' @param vec.size Number specifying the size of vectors.
-#'   (default: \code{vec.size = 0.5})
+#' @param vec.size \code{Numeric scalar}. Specifies the size of vectors.
+#'   (Default: \code{0.5})
 #' 
-#' @param vec.colour String specifying the colour of vectors.
-#'   (default: \code{vec.color = "black"})
+#' @param vec.colour \code{Character scalar}. Specifies the colour of vectors.
+#'   (Default: \code{"black"})
 #' 
 #' @param vec.color Alias for `vec.colour`.
 #' 
-#' @param vec.linetype Discrete number specifying the style of vector lines.
-#'   (default: \code{vec.linetype = 1})
+#' @param vec.linetype \code{Integer scalar}. Specifies the style of vector lines.
+#'   (Default: \code{1})
 #' 
-#' @param arrow.size Number specifying the size of arrows.
+#' @param arrow.size \code{Numeric scalar}. Specifies the size of arrows.
 #'   (defaults: \code{arrow.size = 0.25})
 #' 
-#' @param label.size Number specifying the size of text and labels.
-#'   (default: \code{label.size = 4})
+#' @param label.size \code{Numeric scalar}. Specifies the size of text and labels.
+#'   (Default: \code{4})
 #' 
-#' @param label.colour String specifying the colour of text and labels.
-#'   (default: \code{label.color = "black"})
+#' @param label.colour \code{Character scalar}. Specifies the colour of text and labels.
+#'   (Default: \code{"black"})
 #' 
 #' @param label.color Alias for `label.colour`.
 #' 
-#' @param sep.group String specifying the separator used in the labels.
-#'   (default: \code{sep.group = "\U2014"})
+#' @param sep.group \code{Character scalar}. Specifies the separator used in the labels.
+#'   (Default: \code{"\U2014"})
 #'   
-#' @param repl.underscore String used to replace underscores in the labels.
-#'   (default: \code{repl.underscore = " "})
+#' @param repl.underscore \code{Character scalar}. Used to replace underscores in the labels.
+#'   (Default: \code{" "})
 #' 
-#' @param vec.text TRUE or FALSE, should text instead of labels be used to label vectors.
-#'   (default: \code{vec.text = TRUE})
+#' @param vec.text \code{Logical scalar}. Should text instead of labels be used to label vectors.
+#'   (Default: \code{TRUE})
 #' 
-#' @param repel.labels TRUE or FALSE, should labels be repelled.
-#'   (default: \code{repel.labels = TRUE})
+#' @param repel.labels \code{Logical scalar}. Should labels be repelled.
+#'   (Default: \code{TRUE})
 #'
-#' @param parse.labels TRUE or FALSE, should labels be parsed.
-#'   (default: \code{parse.labels = TRUE})
+#' @param parse.labels \code{Logical scalar}. Should labels be parsed.
+#'   (Default: \code{TRUE})
 #'
-#' @param add.significance TRUE or FALSE, should explained variance and p-value
-#'   appear in the labels. (default: \code{add.significance = TRUE})
+#' @param add.significance \code{Logical scalar}. Should explained variance and p-value
+#'   appear in the labels. (Default: \code{TRUE})
 #'
-#' @param add.expl.var TRUE or FALSE, should explained variance appear on the
-#'   coordinate axes. (default: \code{add.expl.var = TRUE})
+#' @param add.expl.var \code{Logical scalar}. Should explained variance appear on the
+#'   coordinate axes. (Default: \code{TRUE})
 #' 
 #' @param ... additional parameters for plotting, inherited from
 #'   \code{\link[scater:plotReducedDim]{plotReducedDim}},

R/plotColTile.R

@@ -8,12 +8,12 @@
 #'   \code{\link[SummarizedExperiment:SummarizedExperiment-class]{SummarizedExperiment}}
 #'   object.
 #' 
-#' @param x String specifying the column-level metadata field to show on the x-axis.
+#' @param x \code{Character scalar}. Specifies the column-level metadata field to show on the x-axis.
 #'   Alternatively, an \link{AsIs} vector or data.frame, see 
 #'   \code{?\link{retrieveFeatureInfo}} or \code{?\link{retrieveCellInfo}}. Must
 #'   result in a returned \code{character} or \code{factor} vector.
 #'   
-#' @param y String specifying the column-level metadata to show on the y-axis.
+#' @param y \code{Character scalar}. Specifies the column-level metadata to show on the y-axis.
 #'   Alternatively, an \link{AsIs} vector or data.frame, see 
 #'   \code{?\link{retrieveFeatureInfo}} or \code{?\link{retrieveCellInfo}}. Must
 #'   result in a returned \code{character} or \code{factor} vector.

R/plotDMN.R

@@ -6,11 +6,12 @@
 #'   \code{\link[SummarizedExperiment:SummarizedExperiment-class]{SummarizedExperiment}}
 #'   object contain the DMN data in \code{metadata}.
 #'   
-#' @param type the type of measure for access the goodness of fit. One of
+#' @param type \code{Character scalar}. The type of measure for access the goodness of fit. One of
 #'   \sQuote{laplace}, \sQuote{AIC} or \sQuote{BIC}.
 #'
-#' @param name the name to store the result in
+#' @param name \code{Character scalar}. The name to store the result in
 #'   \code{\link[SummarizedExperiment:RangedSummarizedExperiment-class]{metadata}}
+#'   (Default: \code{"DMN"})
 #'
 #' @param ... optional arguments not used.
 #'