Refactoring of do_DotPlot, do_GroupwiseDEPlot and do_TermEnrichmentAn…

…alysis.
enblacar · Feb 6, 2024 · 6ae82ef · 6ae82ef
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commit 6ae82ef
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Showing 8 changed files with 546 additions and 491 deletions.
diff --git a/NEWS.md b/NEWS.md
@@ -18,6 +18,9 @@ The reason of these modification is to allow for a much clearer and concise outp
 ## do_AlluvialPlot()
 -   Enforced a minimum version of `ggalluvial` to deal with deprecation of functions from `dplyr` and `tidyr` that were still used in `ggalluvial` functions.
 
+## do_BoxPlot()
+-   Added `legend.ncol`, `legend.nrow` and `legend.byrow` parameters to control legend behaviour.
+
 ## do_CopyNumberVariantPlot()
 -   Added `include_chr_arms` parameter to decide whether the heatmap should include a breakdown of the arms or just keep it by chromosomes.
 

diff --git a/R/do_BoxPlot.R b/R/do_BoxPlot.R
@@ -36,6 +36,9 @@ do_BoxPlot <- function(sample,
                        legend.title = NULL,
                        legend.title.position = "top",
                        legend.position = "bottom",
+                       legend.ncol = NULL,
+                       legend.nrow = NULL,
+                       legend.byrow = FALSE,
                        boxplot.line.color = "black",
                        outlier.color = "black",
                        outlier.alpha = 0.5,
@@ -76,14 +79,17 @@ do_BoxPlot <- function(sample,
                        "plot.grid" = plot.grid,
                        "order" = order,
                        "use_silhouette" = use_silhouette,
-                       "map_signif_level" = map_signif_level)
+                       "map_signif_level" = map_signif_level,
+                       "legend.byrow" = legend.byrow)
   check_type(parameters = logical_list, required_type = "logical", test_function = is.logical)
   # Check numeric parameters.
   numeric_list <- list("font.size" = font.size,
                        "outlier.alpha" = outlier.alpha,
                        "boxplot.linewidth" = boxplot.linewidth,
                        "boxplot.width" = boxplot.width,
-                       "axis.text.x.angle" = axis.text.x.angle)
+                       "axis.text.x.angle" = axis.text.x.angle,
+                       "legend.nrow" = legend.nrow,
+                       "legend.ncol" = legend.ncol)
   check_type(parameters = numeric_list, required_type = "numeric", test_function = is.numeric)
   # Check character parameters.
   character_list <- list("feature" = feature,
@@ -222,7 +228,10 @@ do_BoxPlot <- function(sample,
                                na.rm = TRUE)   +
          ggplot2::guides(color = ggplot2::guide_legend(title = legend.title,
                                                        title.position = legend.title.position,
-                                                       title.hjust = 0.5))
+                                                       title.hjust = 0.5,
+                                                       ncol = legend.ncol,
+                                                       nrow = legend.nrow,
+                                                       byrow = legend.byrow))
   } else if (isTRUE(use_silhouette) & !is.null(split.by)){
     stop(paste0(add_cross(), crayon_body("Parameter "), crayon_key("use_silhouette"),  crayon_body("can not be used alongside "), crayon_key("split.by"), crayon_body(".")), call. = FALSE)
   } else if (base::isFALSE(use_silhouette)){
@@ -249,7 +258,10 @@ do_BoxPlot <- function(sample,
                                na.rm = TRUE)   +
          ggplot2::guides(fill = ggplot2::guide_legend(title = legend.title,
                                                       title.position = legend.title.position,
-                                                      title.hjust = 0.5))
+                                                      title.hjust = 0.5,
+                                                      ncol = legend.ncol,
+                                                      nrow = legend.nrow,
+                                                      byrow = legend.byrow))
   }
 
    p <- p +

diff --git a/R/do_DotPlot.R b/R/do_DotPlot.R
@@ -230,7 +230,7 @@ do_DotPlot <- function(sample,
     out <- check_cutoffs(min.cutoff = min.cutoff,
                          max.cutoff = max.cutoff,
                          limits = range.data)
-    ragne.data <- out$limits
+    range.data <- out$limits
 
 
     scale.setup <- compute_scales(sample = sample,
@@ -366,7 +366,7 @@ do_DotPlot <- function(sample,
                                   # nocov start
                                   legend.title = if (is.null(legend.title)){"Avg. Expression"} else {legend.title},
                                   # nocov end
-                                  legend.aes = if (isTRUE(dot_border)) {"fill"} else {"color"},
+                                  legend.aes = "fill",
                                   legend.type = legend.type,
                                   legend.position = legend.position,
                                   legend.length = legend.length,