restore usage of removed params in internal fxns

Signed-off-by: Daena Rys <[email protected]>
microbiome · Jun 19, 2024 · 7ffb083 · 7ffb083
1 parent 9b5fda5
commit 7ffb083
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Showing 13 changed files with 380 additions and 189 deletions.
diff --git a/R/plotAbundance.R b/R/plotAbundance.R
@@ -267,8 +267,8 @@ MELT_VALUES <- "Value"
 #' @importFrom tidyr pivot_longer nest unnest
 #' @importFrom tibble rownames_to_column
 #' @importFrom purrr map
-.get_abundance_data <- function(x, rank, assay.type, order.row.by = "name",
-                                use.relative = TRUE){
+.get_abundance_data <- function(x, rank, assay.type, order.row.by = order_rank_by,
+    order_rank_by = "name", use.relative = use_relative, use_relative = TRUE){
     data <- assay(x, assay.type, withDimnames = TRUE)
     if(use.relative){
         data <- mia:::.calc_rel_abund(data)
@@ -322,7 +322,8 @@ MELT_VALUES <- "Value"
     data
 }
 
-.norm_order_sample_by <- function(order.col.by, factors, x){
+.norm_order_sample_by <- function(order.col.by = order_sample_by, 
+    order_sample_by, factors, x){
     if(is.null(order.col.by)){
         return(order.col.by)
     }
@@ -353,7 +354,8 @@ MELT_VALUES <- "Value"
     tmp
 }
 
-.get_features_data <- function(col.var, order.col.by, x){
+.get_features_data <- function(col.var = features, features, 
+    order.col.by = order_sample_by, order_sample_by, x){
     col.var <- unique(c(order.col.by,col.var))
     features_data <- lapply(col.var,
                             .get_feature_data,
@@ -377,7 +379,7 @@ MELT_VALUES <- "Value"
 
 #' @importFrom dplyr pull
 .order_abund_feature_data <- function(abund_data, features_data,
-                                    order.col.by, decreasing = TRUE){
+    order.col.by = order_sample_by, order_sample_by, decreasing = TRUE){
     if(!is.null(order.col.by)){
         lvl <- levels(abund_data$X)
         if(is.null(features_data) || 
@@ -533,13 +535,18 @@ MELT_VALUES <- "Value"
 }
 
 .features_plotter <- function(features_data,
-                            order.col.by = NULL,
+                            order.col.by = order_sample_by,
+                            order_sample_by = NULL,
                             xlab = NULL,
                             flipped = FALSE,
-                            add.legend = TRUE,
-                            add.x.text = FALSE,
-                            point.alpha = 1,
+                            add.legend = add_legend,
+                            add_legend = TRUE,
+                            add.x.text = add_x_text,
+                            add_x_text = FALSE,
+                            point.alpha = point_alpha,
+                            point_alpha = point.size,
                             point.size = 2,
+
                             ...){
     names <- colnames(features_data)
     features_data <- lapply(names, 

diff --git a/R/plotAbundanceDensity.R b/R/plotAbundanceDensity.R
@@ -218,10 +218,14 @@ setMethod("plotAbundanceDensity", signature = c(x = "SummarizedExperiment"),
 ################################ HELP FUNCTIONS ################################
 
 .incorporate_density_data <- function(x, assay.type, n,
-                                      colour.by,
-                                      shape.by,
-                                      size.by,
-                                      order.descending = TRUE){
+                                      colour.by = colour_by,
+                                      colour_by,
+                                      shape.by = shape_by,
+                                      shape_by,
+                                      size.by = size_by,
+                                      size_by,
+                                      order.descending = order_descending,
+                                      order_descending = TRUE){
     # Gets the assay
     mat <- assay(x, assay.type, withDimnames = TRUE)
     # Gets the most abundant taxa
@@ -279,15 +283,21 @@ setMethod("plotAbundanceDensity", signature = c(x = "SummarizedExperiment"),
 
 .density_plotter <- function(density_data, 
                              layout,
-                             add.legend = TRUE,
+                             add.legend = add_legend,
+                             add_legend = TRUE,
                              xlab,
                              ylab = NULL,
-                             colour.by = NULL,
-                             shape.by = NULL,
-                             size.by = NULL,
+                             colour.by = colour_by,
+                             colour_by = NULL,
+                             shape.by = shape_by,
+                             shape_by = NULL,
+                             size.by = size_by,
+                             size_by = NULL,
                              point_shape = 21,
-                             point.size = 2,
-                             point.alpha = 0.6,
+                             point.size = point_size,
+                             point_size = 2,
+                             point.alpha = point_alpha,
+                             point_alpha = 0.6,
                              point_colour = "grey70",
                              flipped = FALSE,
                              scales_free = TRUE,

diff --git a/R/plotCCA.R b/R/plotCCA.R
@@ -301,7 +301,7 @@ setMethod("plotRDA", signature = c(x = "matrix"),
 #' @importFrom scater plotReducedDim retrieveCellInfo
 #' @importFrom SingleCellExperiment reducedDim reducedDimNames
 .incorporate_rda_vis <- function(
-        tse, dimred, ncomponents = 2, colour.by = color_by, color_by = NULL,
+        tse, dimred, ncomponents = 2, colour.by = colour_by, colour_by = color_by, color_by = NULL,
         add.significance = TRUE, add.expl.var = TRUE, add.ellipse = TRUE,
         add.vectors = TRUE, vec.lab = NULL, expl_var = NULL,
         sep.group = "\U2012", repl.underscore = " ", ...){

diff --git a/R/plotColTile.R b/R/plotColTile.R
@@ -145,7 +145,8 @@ setMethod("plotRowTile", signature = c("SummarizedExperiment"),
 }
 
 .tile_plotter <- function(data,
-                          add.legend = TRUE,
+                          add.legend = add_legend,
+                          add_legend = TRUE,
                           xlab,
                           ylab,
                           rect_alpha = 1,

diff --git a/R/plotGraph.R b/R/plotGraph.R
@@ -185,7 +185,8 @@ setGeneric("plotColGraph", signature = c("x","y"),
 setGeneric("plotRowGraph", signature = c("x","y"),
            function(x, y, ...) standardGeneric("plotRowGraph"))
 
-.check_graph_plot_switches <- function(show.label, add_legend){
+.check_graph_plot_switches <- function(show.label = show_label, show_label, 
+    add.legend = add_legend, add_legend){
     if(!.is_a_bool(show.label)){
         if( (!is.logical(show.label) && !is.character(show.label) && 
             !is.numeric(show.label)) ||
@@ -201,7 +202,7 @@ setGeneric("plotRowGraph", signature = c("x","y"),
     }
 }
 
-.norm_layout_edge_type <- function(layout, edge.type){
+.norm_layout_edge_type <- function(layout, edge.type = edge_type, edge_type){
     edge.type <- match.arg(edge.type[1L], c("fan","link","arc","parallel"))
     return(list(layout = layout,
                 edge.type = edge.type))
@@ -227,7 +228,8 @@ setMethod("plotColGraph",
              shape_by = NULL,
              size.by = size_by,
              size_by = NULL,
-             assay.type = "counts",
+             assay.type = by_exprs_values,
+             by_exprs_values = "counts",
              other.fields = other_fields,
              other_fields = list(),
              ...){
@@ -281,7 +283,8 @@ setMethod("plotRowGraph",
              shape.by = shape_by,
              shape_by = NULL,
              size.by = NULL,
-             assay.type = "counts",
+             assay.type = by_exprs_values,
+             by_exprs_values = "counts",
              other.fields = other_fields,
              other_fields = list(),
              ...){
@@ -317,16 +320,25 @@ setMethod("plotRowGraph",
 )
 
 .plot_row_column_graph <- function(x, y,
-                                   show.label = FALSE,
+                                   show.label = show_label,
+                                   show_label = FALSE,
+                                   add.legend = add_legend,
                                    add_legend = TRUE,
                                    layout = "kk",
-                                   edge.type = c("fan","link","arc","parallel"),
-                                   edge.colour.by = NULL,
-                                   edge.width.by = NULL,
+                                   edge.type = edge_type,
+                                   edge_type = c("fan","link","arc","parallel"),
+                                   edge.colour.by = edge_colour_by,
+                                   edge_colour_by = NULL,
+                                   edge.width.by = edge_width_by,
+                                   edge_width_by = NULL,
+                                   colour.by = colour_by,
                                    colour_by = NULL,
-                                   shape.by = NULL,
-                                   size.by = NULL,
-                                   assay.type = "counts",
+                                   shape.by = shape_by,
+                                   shape_by = NULL,
+                                   size.by = size_by,
+                                   size_by = NULL,
+                                   assay.type = by_exprs_values,
+                                   by_exprs_values = "counts",
                                    other.fields = other_fields,
                                    other_fields = list(),
                                    type = c("row","column"),
@@ -382,7 +394,7 @@ setMethod("plotRowGraph",
 
 #' @importFrom tidygraph activate
 #' @importFrom dplyr mutate
-.add_graph_node_labels <- function(graph_data, show.label){
+.add_graph_node_labels <- function(graph_data, show.label = show_label, show_label){
     if(!("label" %in% .colnames_tbl_graph(graph_data, "nodes")) &&
        ("name" %in% .colnames_tbl_graph(graph_data, "nodes"))){
         graph_data <- graph_data %>%
@@ -470,13 +482,20 @@ setMethod("plotRowGraph",
 #' @importFrom tidygraph activate as_tibble
 .incorporate_graph_vis <- function(graph_data,
                                    se,
-                                   edge.colour.by,
-                                   edge.width.by,
+                                   edge.colour.by = edge_colour_by,
+                                   edge_colour_by,
+                                   edge.width.by = edge_width_by,
+                                   edge_width_by,
+                                   colour.by = colour_by,
                                    colour_by,
-                                   shape.by,
-                                   size.by,
-                                   assay.type = "counts",
-                                   other.fields = list(),
+                                   shape.by = shape_by,
+                                   shape_by,
+                                   size.by = size_by,
+                                   size_by,
+                                   assay.type = by_exprs_values,
+                                   by_exprs_values = "counts",
+                                   other.fields = other_fields,
+                                   other_fields = list(),
                                    type = c("row","column")){
     type <- match.arg(type)
     type_FUN <- switch(type,
@@ -576,20 +595,34 @@ setMethod("plotRowGraph",
 
 .graph_plotter <- function(object,
                            layout = "kk",
-                           edge.type = "fan",
+                           edge.type = edge_type,
+                           edge_type = "fan",
                            algorithm = NULL,
+                           add.legend = add_legend,
                            add_legend = TRUE,
-                           show.label = FALSE,
-                           edge.colour.by = NULL,
-                           edge.width.by = NULL,
+                           show.label = show_label,
+                           show_label = FALSE,
+                           edge.colour.by = edge_colour_by,
+                           edge_colour_by = NULL,
+                           edge.width.by = edge_width_by,
+                           edge_width_by = NULL,
+                           colour.by = colour_by,
                            colour_by = NULL,
-                           shape.by = NULL,
-                           size.by = NULL,
+                           shape.by = shape_by,
+                           shape_by = NULL,
+                           size.by = size_by,
+                           size_by = NULL,
+                           line.alpha = line_alpha,
                            line_alpha = 1,
+                           line.width = line_width,
                            line_width = NULL,
+                           line.width.range = line_width_range,
                            line_width_range = c(0.5,3),
-                           point.alpha = 1,
-                           point.size = 2,
+                           point.alpha = point_alpha,
+                           point_alpha = 1,
+                           point.size = point_size,
+                           point_size = 2,
+                           point.size.range = point_size_range,
                            point_size_range = c(1,4)){
     # assemble arg list
     point_out <- .get_point_args(colour_by,
@@ -669,7 +702,7 @@ setMethod("plotRowGraph",
 }
 
 #' @importFrom tidyr drop_na
-.add_graph_labels <- function(plot_out, show.label){
+.add_graph_labels <- function(plot_out, show.label = show_label, show_label){
     label <- NULL # disable note: no global binding for variable
     if(show.label){
         label_data <- plot_out$data %>% drop_na(label)

diff --git a/R/plotPrevalence.R b/R/plotPrevalence.R
@@ -198,8 +198,8 @@ setMethod("plotPrevalence", signature = c(x = "SummarizedExperiment"),
 #' @importFrom BiocParallel bpmapply bpisup bpstart bpstop SerialParam
 #' @importFrom SummarizedExperiment assay
 .get_prevalence_plot_data <- function(x, assay.type, detections, prevalences,
-                                      as.relative = TRUE, 
-                                      BPPARAM = BiocParallel::SerialParam()){
+    as.relative = as_relative, as_relative = TRUE,
+    BPPARAM = BiocParallel::SerialParam()){
     mat <- assay(x, assay.type, withDimnames = TRUE)
     if(as.relative){
         mat <- mia:::.calc_rel_abund(mat)
@@ -233,8 +233,8 @@ setMethod("plotPrevalentAbundance", signature = c(x = "SummarizedExperiment"),
     function(x,
              rank = taxonomyRanks(x)[1L],
              assay.type = assay_name, assay_name = "counts",
-             as.relative = TRUE,
-             colour.by = NULL,
+             as.relative = as_relative, as_relative = TRUE,
+             colour.by = colour_by, colour_by = NULL,
              size.by = size_by,
              size_by = NULL,
              shape.by = shape_by,
@@ -298,8 +298,8 @@ setMethod("plotPrevalentAbundance", signature = c(x = "SummarizedExperiment"),
 
 #' @importFrom DelayedArray rowMeans
 #' @importFrom SummarizedExperiment assay
-.get_prevalence_plot_point_data <- function(x, assay.type, as.relative = TRUE,
-                                            label = NULL){
+.get_prevalence_plot_point_data <- function(x, assay.type, as.relative = as_relative, 
+    as_relative = TRUE, label = NULL){
     mat <- assay(x, assay.type, withDimnames = TRUE)
     if(as.relative){
         mat <- mia:::.calc_rel_abund(mat)
@@ -314,13 +314,14 @@ setMethod("plotPrevalentAbundance", signature = c(x = "SummarizedExperiment"),
 }
 
 #' @importFrom scater retrieveFeatureInfo
-.incorporate_prevalence_vis <- function(plot_data,
+.incorporate_prevalence_vis <- function(plot.data = plot_data,
+                                        plot_data,
                                         se = se,
-                                        colour.by = NULL,
-                                        size.by = NULL,
-                                        shape.by = NULL,
+                                        colour.by = colour_by, colour_by = NULL,
+                                        size.by = size_by, size_by = NULL,
+                                        shape.by = shape_by, shape_by = NULL,
                                         label = NULL,
-                                        facet.by = NULL){
+                                        facet.by = facet_by, facet_by = NULL){
     variables <- c(colour.by = colour.by,
                    size.by = size.by,
                    shape.by = shape.by,
@@ -434,8 +435,8 @@ setMethod("plotFeaturePrevalence", signature = c(x = "SummarizedExperiment"),
 #' @importFrom tidyr pivot_longer
 #' @importFrom DelayedArray rowSums
 .get_prevalence_plot_matrix <- function(x, assay.type, detections, 
-                                        as.relative = TRUE, 
-                                        min.prevalence,
+                                        as.relative = as_relative, as_relative = TRUE,
+                                        min.prevalence = min_prevalence, min_prevalence,
                                         BPPARAM = BiocParallel::SerialParam()){
     mat <- assay(x, assay.type, withDimnames = TRUE)
     if(as.relative){

diff --git a/R/plotSeries.R b/R/plotSeries.R
@@ -211,7 +211,8 @@ setMethod("plotSeries", signature = c(object = "SummarizedExperiment"),
     return(assay)
 }
 
-.incorporate_series_vis <- function(object, x, colour.by, linetype_by, size.by){
+.incorporate_series_vis <- function(object, x, colour.by = colour_by, colour_by, 
+    linetype_by, size.by = size_by, size_by){
 
     # This variable is set by defaults
     series_data <- retrieveCellInfo(object, x, search = "colData")
@@ -296,14 +297,23 @@ setMethod("plotSeries", signature = c(object = "SummarizedExperiment"),
 .series_plotter <- function(plot_data,
                             xlab = NULL,
                             ylab = NULL,
-                            colour.by = NULL,
+                            colour.by = colour_by,
+                            colour_by = NULL,
+                            linetype.by = linetype_by,
                             linetype_by = NULL,
-                            size.by = NULL,
-                            add.legend = TRUE,
+                            size.by = size_by,
+                            size_by = NULL,
+                            add.legend = add_legend,
+                            add_legend = TRUE,
+                            line.alpha = line_alpha,
                             line_alpha = 1,
+                            line.type = line_type,
                             line_type = NULL,
+                            line.width = line_width,
                             line_width = 1,
+                            line.width.range = line_width_range,
                             line_width_range = c(0.5,3),
+                            ribbon.alpha = ribbon_alpha,
                             ribbon_alpha = 0.3){
     # fall back for feature grouping
     if(is.null(colour.by)){
@@ -361,7 +371,8 @@ setMethod("plotSeries", signature = c(object = "SummarizedExperiment"),
     plot_out
 }
 
-.add_extra_line_guide <- function(plot_out, linetype_by, size.by) {
+.add_extra_line_guide <- function(plot.out = plot_out, plot_out, 
+    linetype.by = linetype_by, linetype_by, size.by = size_by, size_by) {
     guide_args <- list()
     if (!is.null(linetype_by)) {
         guide_args$linetype <- guide_legend(title = linetype_by)