docs: fix cross-links to plotthis functions

Author: pwwang

R/cccplot.R

@@ -61,11 +61,11 @@
 #' @param show_column_names Whether to show the column names in the heatmap. Default is TRUE.
 #'  Only used when `plot_type` is "heatmap".
 #' @param ... Other arguments passed to the specific plot function.
-#'  * For `Network`, see [plotthis::Network].
-#'  * For `ChordPlot`, see [plotthis::ChordPlot].
-#'  * For `Heatmap`, see [plotthis::Heatmap].
-#'  * For `SankeyPlot`, see [plotthis::SankeyPlot].
-#'  * For `DotPlot`, see [plotthis::DotPlot].
+#'  * For `Network`, see [plotthis::Network()].
+#'  * For `ChordPlot`, see [plotthis::ChordPlot()].
+#'  * For `Heatmap`, see [plotthis::Heatmap()].
+#'  * For `SankeyPlot`, see [plotthis::SankeyPlot()].
+#'  * For `DotPlot`, see [plotthis::DotPlot()].
 #' @return A ggplot object or a list if `combine` is FALSE
 #' @importFrom utils getFromNamespace
 #' @importFrom rlang syms sym

R/celldimplot.R

@@ -4,7 +4,7 @@
 #' @param object A seurat object
 #' @param reduction Name of the reduction to plot (for example, "umap").
 #' @param graph Specify the graph name to add edges between cell neighbors to the plot.
-#' @param ... Other arguments passed to [plotthis::DimPlot].
+#' @param ... Other arguments passed to [plotthis::DimPlot()].
 #' @return A ggplot object or a list if `combine` is FALSE
 #' @export
 #' @importFrom SeuratObject DefaultDimReduc Embeddings Graphs Reductions

R/cellstatplot.R

@@ -50,19 +50,19 @@
 #' @param name The name of the 'pies'/'heatmap' plot, shown as the name of the main legend. Default is NULL.
 #' @param ylab The y-axis label. Default is NULL.
 #' @param ... Other arguments passed to the specific plot function.
-#'   * For `bar` plot, see [plotthis::BarPlot].
-#'   * For `circos` plot, see [plotthis::CircosPlot].
-#'   * For `pie` chart, see [plotthis::PieChart].
-#'   * For `pies` plot, see [plotthis::Heatmap].
-#'   * For `heatmap` plot, see [plotthis::Heatmap].
-#'   * For `ring`/`donut` plot, see [plotthis::RingPlot].
-#'   * For `trend` plot, see [plotthis::TrendPlot].
-#'   * For `area` plot, see [plotthis::AreaPlot].
-#'   * For `sankey`/`alluvial` plot, see [plotthis::SankeyPlot].
-#'   * For `radar` plot, see [plotthis::RadarPlot].
-#'   * For `spider` plot, see [plotthis::SpiderPlot].
-#'   * For `violin` plot, see [plotthis::ViolinPlot].
-#'   * For `box` plot, see [plotthis::BoxPlot].
+#'   * For `bar` plot, see [plotthis::BarPlot()].
+#'   * For `circos` plot, see [plotthis::CircosPlot()].
+#'   * For `pie` chart, see [plotthis::PieChart()].
+#'   * For `pies` plot, see [plotthis::Heatmap()].
+#'   * For `heatmap` plot, see [plotthis::Heatmap()].
+#'   * For `ring`/`donut` plot, see [plotthis::RingPlot()].
+#'   * For `trend` plot, see [plotthis::TrendPlot()].
+#'   * For `area` plot, see [plotthis::AreaPlot()].
+#'   * For `sankey`/`alluvial` plot, see [plotthis::SankeyPlot()].
+#'   * For `radar` plot, see [plotthis::RadarPlot()].
+#'   * For `spider` plot, see [plotthis::SpiderPlot()].
+#'   * For `violin` plot, see [plotthis::ViolinPlot()].
+#'   * For `box` plot, see [plotthis::BoxPlot()].
 #'
 #' @return A ggplot object or a list if `combine` is FALSE
 #' @importFrom rlang sym syms

R/clonaldivplot.R

@@ -104,9 +104,9 @@ ClonalDiversity <- function(
 #' @param xlab The x-axis label. Default is NULL.
 #' @param ylab The y-axis label. Default is NULL.
 #' @param ... Other arguments passed to the specific plot function.
-#'  * For "bar", [plotthis::BarPlot]
-#'  * For "box", [plotthis::BoxPlot]
-#'  * For "violin", [plotthis::ViolinPlot]
+#'  * For "bar", [plotthis::BarPlot()].
+#'  * For "box", [plotthis::BoxPlot()].
+#'  * For "violin", [plotthis::ViolinPlot()].
 #' @return A ggplot object or a list if `combine` is FALSE
 #' @export
 #' @importFrom tidyr separate
@@ -214,7 +214,7 @@ ClonalDiversityPlot <- function(
 #' @param nrow The number of rows in the combined plot. Default is NULL.
 #' @param ncol The number of columns in the combined plot. Default is NULL.
 #' @param byrow Whether to fill the combined plot by row. Default is TRUE.
-#' @param ... Other arguments passed to [plotthis::RarefactionPlot].
+#' @param ... Other arguments passed to [plotthis::RarefactionPlot()].
 #' @return A ggplot object or a list if `combine` is FALSE
 #' @importFrom plotthis RarefactionPlot
 #' @export

R/clonalgeneusageplot.R

@@ -22,10 +22,10 @@
 #' @param row_annotation_side The side of the row annotation. Default is "right".
 #' @param row_annotation_agg A list of row annotation aggregation functions.
 #' @param ... Other arguments passed to the specific plot function.
-#'  * For "bar", [plotthis::BarPlot]
-#'  * For "heatmap", [plotthis::Heatmap]
-#'  * For "circos", [plotthis::ChordPlot]
-#'  * For "chord", [plotthis::ChordPlot]
+#'  * For "bar", [plotthis::BarPlot()].
+#'  * For "heatmap", [plotthis::Heatmap()].
+#'  * For "circos", [plotthis::ChordPlot()].
+#'  * For "chord", [plotthis::ChordPlot()].
 #' @return A ggplot object or a list if `combine` is FALSE
 #' @importFrom rlang := syms
 #' @importFrom dplyr mutate rename slice_max summarise pull filter all_of

R/clonalpositionalplot.R

@@ -35,11 +35,11 @@
 #' @param facet_nrow The number of rows in the facet grid. Default is NULL.
 #' @param aspect.ratio The aspect ratio of the plot. Default is NULL.
 #' @param ... Other arguments passed to the specific plot function.
-#'  * For "bar", [plotthis::BarPlot]
-#'  * For "line", [plotthis::LinePlot]
-#'  * For "heatmap", [plotthis::Heatmap]
-#'  * For "box", [plotthis::BoxPlot]
-#'  * For "violin", [plotthis::ViolinPlot]
+#'  * For "bar", [plotthis::BarPlot()].
+#'  * For "line", [plotthis::LinePlot()].
+#'  * For "heatmap", [plotthis::Heatmap()].
+#'  * For "box", [plotthis::BoxPlot()].
+#'  * For "violin", [plotthis::ViolinPlot()].
 #' @return A ggplot object or a list if `combine` is FALSE
 #' @export
 #' @importFrom ggplot2 element_blank
@@ -220,9 +220,9 @@ ClonalPositionalPlot <- function (
 #' @param aspect.ratio The aspect ratio of the plot. Default is NULL.
 #' @param facet_ncol The number of columns in the facet grid. Default is NULL.
 #' @param ... Other arguments passed to the specific plot function.
-#'  * For "bar", [plotthis::BarPlot]
-#'  * For "line", [plotthis::LinePlot]
-#'  * For "heatmap", [plotthis::Heatmap]
+#'  * For "bar", [plotthis::BarPlot()].
+#'  * For "line", [plotthis::LinePlot()].
+#'  * For "heatmap", [plotthis::Heatmap()].
 #' @return A ggplot object or a list if `combine` is FALSE
 #' @export
 #' @importFrom tidyr pivot_longer separate unite

R/clonalstatplot.R

@@ -20,9 +20,9 @@
 #' @param order The order of the x-axis items or groups. Default is an empty list.
 #'  It should be a list of values. The names are the column names, and the values are the order.
 #' @param ... Other arguments passed to the specific plot function.
-#'  * For `bar` plot, see [plotthis::BarPlot].
-#'  * For `box` plot, see [plotthis::BoxPlot].
-#'  * For `violin` plot, see [plotthis::ViolinPlot].
+#'  * For `bar` plot, see [plotthis::BarPlot()].
+#'  * For `box` plot, see [plotthis::BoxPlot()].
+#'  * For `violin` plot, see [plotthis::ViolinPlot()].
 #' @return A ggplot object or a list if `combine` is FALSE
 #' @importFrom tidyr separate
 #' @importFrom plotthis BarPlot BoxPlot ViolinPlot
@@ -143,9 +143,9 @@ ClonalVolumePlot <- function(
 #' @param ytrans The transformation to apply to the y-axis. Default is "identity".
 #' @param theme_args The theme arguments to be passed to the plot function.
 #' @param ... Other arguments passed to the specific plot function.
-#'  * For `trend` plot, see [plotthis::Histogram].
-#'  * For `histogram` plot, see [plotthis::Histogram].
-#'  * For `density` plot, see [plotthis::DensityPlot].
+#'  * For `trend` plot, see [plotthis::Histogram()].
+#'  * For `histogram` plot, see [plotthis::Histogram()].
+#'  * For `density` plot, see [plotthis::DensityPlot()].
 #' @return A ggplot object or a list if `combine` is FALSE
 #' @importFrom tidyr full_seq complete
 #' @importFrom dplyr group_modify
@@ -234,7 +234,7 @@ ClonalAbundancePlot <- function(
 #' @param chain indicate if both or a specific chain should be used - e.g. "both",
 #'  "TRA", "TRB", "TRD", "TRG", "IGH", or "IGL" to specify a specific chain.
 #' @param plot_type The type of plot to use. Default is "bar".
-#'  Possible values are "histogram" and "density".
+#'  Possible values are "box", "violin" and "density".
 #' @param x_nbreaks The number of breaks for the x-axis. Default is 10.
 #' @param group_by The column name in the meta data to group the cells. Default: "Sample"
 #' @param facet_by The column name in the meta data to facet the plots. Default: NULL
@@ -245,7 +245,10 @@ ClonalAbundancePlot <- function(
 #' @param ylab The y-axis label.
 #' @param position The position of the bars for bar plot on the x-axis. Default is "dodge".
 #' @param ... Other arguments passed to the specific plot function.
-#'  * For
+#' * For `bar` plot, see [plotthis::BarPlot()].
+#' * For `box` plot, see [plotthis::BoxPlot()].
+#' * For `violin` plot, see [plotthis::ViolinPlot()].
+#' * For `density` plot, see [plotthis::DensityPlot()].
 #' @return A ggplot object or a list if `combine` is FALSE
 #' @importFrom stats quantile
 #' @importFrom rlang syms
@@ -601,9 +604,9 @@ DummyClonalScatterPlot <- function(df, title, group_by, scatter_cor, size_by, ..
 #' @param ncol The number of columns in the combined plot. Default is NULL.
 #' @param byrow Whether to fill the combined plot by row. Default is TRUE.
 #' @param ... Other arguments passed to the specific plot function.
-#'  * For `scatter` plot, see [plotthis::ScatterPlot].
-#'  * For `venn` plot, see [plotthis::VennDiagram].
-#'  * For `upset` plot, see [plotthis::UpsetPlot].
+#'  * For `scatter` plot, see [plotthis::ScatterPlot()].
+#'  * For `venn` plot, see [plotthis::VennDiagram()].
+#'  * For `upset` plot, see [plotthis::UpsetPlot()].
 #' @return A ggplot object or a list if `combine` is FALSE
 #' @export
 #' @importFrom utils combn
@@ -783,10 +786,10 @@ ClonalResidencyPlot <- function(
 #' @param order The order of the x-axis items or groups. Default is an empty list.
 #'  It should be a list of values. The names are the column names, and the values are the order.
 #' @param ... Other arguments passed to the specific plot function.
-#'  * For `bar` plot, see [plotthis::BarPlot].
-#'  * For `ring` plot, see [plotthis::RingPlot].
-#'  * For `box` plot, see [plotthis::BoxPlot].
-#'  * For `violin` plot, see [plotthis::ViolinPlot].
+#'  * For `bar` plot, see [plotthis::BarPlot()].
+#'  * For `ring` plot, see [plotthis::RingPlot()].
+#'  * For `box` plot, see [plotthis::BoxPlot()].
+#'  * For `violin` plot, see [plotthis::ViolinPlot()].
 #' @return A ggplot object or a list if `combine` is FALSE
 #' @importFrom dplyr %>% mutate summarise ungroup n
 #' @importFrom tidyr pivot_longer separate
@@ -981,7 +984,7 @@ ClonalCompositionPlot <- function(
 #' @param cluster_columns Whether to cluster the columns. Default is FALSE.
 #' @param show_row_names Whether to show the row names. Default is TRUE.
 #' @param show_column_names Whether to show the column names. Default is TRUE.
-#' @param ... Other arguments passed to the specific plot function [plotthis::Heatmap].
+#' @param ... Other arguments passed to the specific plot function [plotthis::Heatmap()].
 #' @return A ComplexHeatmap object or a list if `combine` is FALSE
 #' @importFrom stats as.dist
 #' @importFrom rlang syms
@@ -1111,8 +1114,8 @@ ClonalOverlapPlot <- function(
 #' @param orderby An expression to order the clones by. Default is NULL.
 #' Note that the clones will be ordered by the value of this expression in descending order.
 #' @param ... Other arguments passed to the specific plot function.
-#'  * For `chord` plot, see [plotthis::ChordPlot].
-#'  * For `sankey` plot, see [plotthis::SankeyPlot].
+#'  * For `trend` plot, see [plotthis::TrendPlot()].
+#'  * For `sankey` plot, see [plotthis::SankeyPlot()].
 #' @return A ggplot object or a list if `combine` is FALSE
 #' @importFrom rlang parse_expr
 #' @importFrom dplyr %>% summarise arrange desc mutate rename

R/clustreeplot.R

@@ -3,7 +3,7 @@
 #'
 #' @description This function generates a clustree plot from a data frame or a Seurat object.
 #' @param object The data frame or Seurat object
-#' @param ... Other arguments passed to [plotthis::ClustreePlot]
+#' @param ... Other arguments passed to [plotthis::ClustreePlot()]
 #' @return A ggplot object or a list if `combine` is FALSE
 #' @export
 #' @examples

R/enrichmentplot.R

@@ -45,13 +45,13 @@
 #' @param xlab The x-axis label. Default is NULL.
 #' @param ylab The y-axis label. Default is NULL.
 #' @param ... Other arguments passed to the specific plot function.
-#'  * For "bar", [plotthis::BarPlot]
-#'  * For "dot", [plotthis::DotPlot]
-#'  * For "lollipop", [plotthis::LollipopPlot]
-#'  * For "network", [plotthis::EnrichNetwork]
-#'  * For "enrichmap", [plotthis::EnrichMap]
-#'  * For "wordcloud", [plotthis::WordCloudPlot]
-#'  * For "comparison", [plotthis::DotPlot]
+#'  * For "bar", [plotthis::BarPlot()].
+#'  * For "dot", [plotthis::DotPlot()].
+#'  * For "lollipop", [plotthis::LollipopPlot()].
+#'  * For "network", [plotthis::EnrichNetwork()].
+#'  * For "enrichmap", [plotthis::EnrichMap()].
+#'  * For "wordcloud", [plotthis::WordCloudPlot()].
+#'  * For "comparison", [plotthis::DotPlot()].
 #' @importFrom rlang sym syms
 #' @importFrom stringr str_wrap
 #' @importFrom dplyr %>% group_by slice_min ungroup

R/featurestatplot.R

@@ -20,15 +20,15 @@
 #' @param ylab The y-axis label.
 #' @param x_text_angle The angle of the x-axis text. Only used when `plot_type` is "violin", "bar", or "box".
 #' @param ... Other arguments passed to the plot functions.
-#'  * For `plot_type` "violin", the arguments are passed to [plotthis::ViolinPlot].
-#'  * For `plot_type` "box", the arguments are passed to [plotthis::BoxPlot].
-#'  * For `plot_type` "bar", the arguments are passed to [plotthis::BarPlot].
-#'  * For `plot_type` "ridge", the arguments are passed to [plotthis::RidgePlot].
-#'  * For `plot_type` "dim", the arguments are passed to [plotthis::FeatureDimPlot].
-#'  * For `plot_type` "heatmap", the arguments are passed to [plotthis::Heatmap].
-#'  * For `plot_type` "cor" with 2 features, the arguments are passed to [plotthis::CorPlot].
-#'  * For `plot_type` "cor" with more than 2 features, the arguments are passed to [plotthis::CorPairsPlot].
-#'  * For `plot_type` "dot", the arguments are passed to [plotthis::Heatmap] with `cell_type` set to "dot".
+#'  * For `plot_type` "violin", the arguments are passed to [plotthis::ViolinPlot()].
+#'  * For `plot_type` "box", the arguments are passed to [plotthis::BoxPlot()].
+#'  * For `plot_type` "bar", the arguments are passed to [plotthis::BarPlot()].
+#'  * For `plot_type` "ridge", the arguments are passed to [plotthis::RidgePlot()].
+#'  * For `plot_type` "dim", the arguments are passed to [plotthis::FeatureDimPlot()].
+#'  * For `plot_type` "heatmap", the arguments are passed to [plotthis::Heatmap()].
+#'  * For `plot_type` "cor" with 2 features, the arguments are passed to [plotthis::CorPlot()].
+#'  * For `plot_type` "cor" with more than 2 features, the arguments are passed to [plotthis::CorPairsPlot()].
+#'  * For `plot_type` "dot", the arguments are passed to [plotthis::Heatmap()] with `cell_type` set to "dot".
 #' @return A ggplot object or a list if `combine` is FALSE
 #' @export
 #' @importFrom rlang %||% syms