Add a plethora of tiny enhancements. See NEWS.md

NEWS.md

@@ -5,36 +5,47 @@ Take this a teaser of things to come in the next version.
 ## General changes
 
 -   Change color palette when using `enforce_symmetry = TRUE` to have the middle color as `grey95` instead of the previous one, which made middle values seem closer to the positive end of the scale.
-- Modify internal structure of all functions to abide with [tidyselect v1.2.0 lifecycle modifications](https://tidyselect.r-lib.org/news/index.html#lifecycle-changes-1-2-0).
+-   Modified internal structure of all functions to abide with [tidyselect v1.2.0 lifecycle modifications](https://tidyselect.r-lib.org/news/index.html#lifecycle-changes-1-2-0).
+-   Modified `rotate_x_axis_labels` parameter in all functions that made use of it. Now, instead of accepting a `logical`, accepts a `numeric`: either `0`, `45` or `90`, corresponding to the degrees in which the X axis labels should be rotated. ([#5](https://github.com/enblacar/SCpubr/issues/5#issuecomment-1289203453))
 
 ## `SCpubr::do_CopyNumberVariantPlot`
 
 -   Modified the code for `SCpubr::do_CopyNumberVariantPlot` to also report results for the whole chromosome as well as for each chromosome arm.
 -   Include the `verbose` argument to `SCpubr::do_CopyNumberVariantPlot` to silence the messages when there are not enough genes in the chromosome to perform the analysis.
 
 ## `SCpubr::do_DimPlot()`
-
 -   Fixed a typo that prevented labels to be bold in `SCpubr::do_DimPlot()` when cell borders are displayed.
 -   Added `group.by` and `split.by` functionality to `SCpubr::do_DimPlot()`. ([#4](https://github.com/enblacar/SCpubr/issues/4))
 
-## `SCpubr::do_FeaturePlot()`
+## `SCpubr::do_DotPLot()`
+-   Added ticks to axes.
+-   Modified default colors to convey a better aesthetic. 
 
+## `SCpubr::do_FeaturePlot()`
 -   Fixed potential bugs in `SCpubr::do_FeaturePlot` when setting `enforce_symmetry = TRUE`.
 -   Changed default value of `order` in `SCpubr::do_FeaturePlot()` from `TRUE` to `FALSE`.
 -   Added `min.cutoff` and `max.cutoff` parameters to `SCpubr::do_FeaturePlot()`. This allows to effectively subset the color scale to the values provided. Cells outside the range will be converted to the min or max values provided, respectively. ([#2](https://github.com/enblacar/SCpubr/issues/2))
 
-## `SCpubr::do_GroupwiseDEPlot()`
+## `SCpubr::do_GeyserPlot()`
+-   Added `flip` parameter.
 
+## `SCpubr::do_GroupwiseDEPlot()`
 -   Fixed bug in `SCpubr::do_GroupwiseDEPlot` in which the heatmap could not be computed. ([#3](https://github.com/enblacar/SCpubr/issues/3))
 -   Added extra checks to ensure proper input in `SCpubr::do_GroupwiseDEPlot`. ([#3](https://github.com/enblacar/SCpubr/issues/3))
 
-## `SCpubr::do_RidgePlot()`
+## `SCpubr::do_LigandReceptorPlot()` (development release)
+- Changed parameter `x_labels_angle` to `rotate_x_axis_labels` to keep a consistent terminology.
 
+## `SCpubr::do_RidgePlot()`
 -   Fixed a typo that made the lines in `panel.grid.minor` to be displayed in `SCpubr::do_Ridgeplot()`.
+-   Added `flip` parameter.
 
 ## `SCpubr::do_ViolinPlot()`
-
 -   Added `split.by` functionality to `SCpubr::do_ViolinPlot()`. ([#4](https://github.com/enblacar/SCpubr/issues/4), [#5](https://github.com/enblacar/SCpubr/issues/5))
+-   Added `flip` parameter.
+-   Now multiple features can be queried ad the same time. ([#5](https://github.com/enblacar/SCpubr/issues/5#issuecomment-1289203453))
+-   Changed `feature` parameter to `features`, to better reflect the multiple feature behavior.
+-   Recreated `Seurat`'s `share.y.lims` behavior and set it to `share.y.lims` parameter. ([#5](https://github.com/enblacar/SCpubr/issues/5#issuecomment-1289203453))
 
 # SCpubr v1.0.1
 

R/do_BarPlot.R

@@ -23,7 +23,7 @@ do_BarPlot <- function(sample,
                        font.size = 14,
                        font.type = "sans",
                        legend.position = "bottom",
-                       rotate_x_axis_labels = TRUE,
+                       rotate_x_axis_labels = 45,
                        legend.title = NULL,
                        xlab = NULL,
                        ylab = NULL,
@@ -43,12 +43,12 @@ do_BarPlot <- function(sample,
 
   # Check logical parameters.
   logical_list <- list("order" = order,
-                       "rotate_x_axis_labels" = rotate_x_axis_labels,
                        "flip" = flip,
                        "plot.grid" = plot.grid)
   check_type(parameters = logical_list, required_type = "logical", test_function = is.logical)
   # Check numeric parameters.
-  numeric_list <- list("font.size" = font.size)
+  numeric_list <- list("font.size" = font.size,
+                       "rotate_x_axis_labels" = rotate_x_axis_labels)
   check_type(parameters = numeric_list, required_type = "numeric", test_function = is.numeric)
   # Check character parameters.
 
@@ -73,6 +73,7 @@ do_BarPlot <- function(sample,
   check_parameters(parameter = font.type, parameter_name = "font.type")
   check_parameters(parameter = legend.position, parameter_name = "legend.position")
   check_parameters(parameter = grid.type, parameter_name = "grid.type")
+  check_parameters(parameter = rotate_x_axis_labels, parameter_name = "rotate_x_axis_labels")
 
   # Get the general table.
   assertthat::assert_that(class(sample@meta.data[, group.by]) %in% c("character", "factor"),
@@ -124,9 +125,9 @@ do_BarPlot <- function(sample,
                       axis.line.y = if (isTRUE(flip)) {ggplot2::element_line(color = "black")} else if (isFALSE(flip)) {ggplot2::element_blank()},
                       axis.text.x = ggplot2::element_text(color = "black",
                                                           face = "bold",
-                                                          angle = ifelse(isTRUE(rotate_x_axis_labels), 45, 0),
-                                                          hjust = ifelse(isTRUE(rotate_x_axis_labels), 1, 0.5),
-                                                          vjust = ifelse(isTRUE(rotate_x_axis_labels), 1, 1)),
+                                                          angle = get_axis_parameters(angle = rotate_x_axis_labels, flip = flip)[["angle"]],
+                                                          hjust = get_axis_parameters(angle = rotate_x_axis_labels, flip = flip)[["hjust"]],
+                                                          vjust = get_axis_parameters(angle = rotate_x_axis_labels, flip = flip)[["vjust"]]),
                       axis.text.y = ggplot2::element_text(color = "black", face = "bold"),
                       axis.ticks = ggplot2::element_line(color = "black"),
                       plot.title.position = "plot",

R/do_BoxPlot.R

@@ -26,7 +26,7 @@ do_BoxPlot <- function(sample,
                        slot = "data",
                        font.size = 14,
                        font.type = "sans",
-                       rotate_x_axis_labels = TRUE,
+                       rotate_x_axis_labels = 45,
                        colors.use = NULL,
                        na.value = "grey75",
                        plot.title = NULL,
@@ -65,7 +65,6 @@ do_BoxPlot <- function(sample,
   slot <- check_and_set_slot(slot = slot)
   # Check logical parameters.
   logical_list <- list("flip" = flip,
-                       "rotate_x_axis_labels" = rotate_x_axis_labels,
                        "plot.grid" = plot.grid,
                        "order" = order,
                        "use_silhouette" = use_silhouette,
@@ -75,7 +74,8 @@ do_BoxPlot <- function(sample,
   numeric_list <- list("font.size" = font.size,
                        "outlier.alpha" = outlier.alpha,
                        "boxplot.linewidth" = boxplot.linewidth,
-                       "boxplot.width" = boxplot.width)
+                       "boxplot.width" = boxplot.width,
+                       "rotate_x_axis_labels" = rotate_x_axis_labels)
   check_type(parameters = numeric_list, required_type = "numeric", test_function = is.numeric)
   # Check character parameters.
   character_list <- list("feature" = feature,
@@ -115,7 +115,7 @@ do_BoxPlot <- function(sample,
   check_parameters(parameter = font.type, parameter_name = "font.type")
   check_parameters(parameter = legend.position, parameter_name = "legend.position")
   check_parameters(parameter = grid.type, parameter_name = "grid.type")
-
+  check_parameters(parameter = rotate_x_axis_labels, parameter_name = "rotate_x_axis_labels")
 
   if (is.null(group.by)){
     sample[["group.by"]] <- Seurat::Idents(sample)
@@ -220,9 +220,9 @@ do_BoxPlot <- function(sample,
                        axis.line.y = if (isTRUE(flip)) {ggplot2::element_line(color = "black")} else if (isFALSE(flip)) {ggplot2::element_blank()},
                        axis.text.x = ggplot2::element_text(color = "black",
                                                            face = "bold",
-                                                           angle = ifelse(isTRUE(rotate_x_axis_labels), 45, 0),
-                                                           hjust = ifelse(isTRUE(rotate_x_axis_labels), 1, 0.5),
-                                                           vjust = ifelse(isTRUE(rotate_x_axis_labels), 1, 1)),
+                                                           angle = get_axis_parameters(angle = rotate_x_axis_labels, flip = flip)[["angle"]],
+                                                           hjust = get_axis_parameters(angle = rotate_x_axis_labels, flip = flip)[["hjust"]],
+                                                           vjust = get_axis_parameters(angle = rotate_x_axis_labels, flip = flip)[["vjust"]]),
                        axis.text.y = ggplot2::element_text(color = "black", face = "bold"),
                        axis.ticks = ggplot2::element_line(color = "black"),
                        panel.grid.major = ggplot2::element_blank(),

R/do_CopyNumberVariantPlot.R

@@ -32,7 +32,7 @@ do_CopyNumberVariantPlot <- function(sample,
                                      font.type = "sans",
                                      border.size = 2,
                                      border.color = "black",
-                                     rotate_x_axis_labels = TRUE,
+                                     rotate_x_axis_labels = 45,
                                      plot_cell_borders = TRUE,
                                      enforce_symmetry = TRUE,
                                      legend.title = NULL,
@@ -44,7 +44,6 @@ do_CopyNumberVariantPlot <- function(sample,
 
   # Check logical parameters.
   logical_list <- list("using_metacells" = using_metacells,
-                       "rotate_x_axis_labels" = rotate_x_axis_labels,
                        "enforce_symmetry" = enforce_symmetry,
                        "plot_cell_borders" = plot_cell_borders)
   check_type(parameters = logical_list, required_type = "logical", test_function = is.logical)
@@ -56,7 +55,8 @@ do_CopyNumberVariantPlot <- function(sample,
                        "legend.tickwidth" = legend.tickwidth,
                        "pt.size" = pt.size,
                        "border.size" = border.size,
-                       "viridis_direction" = viridis_direction)
+                       "viridis_direction" = viridis_direction,
+                       "rotate_x_axis_labels" = rotate_x_axis_labels)
   check_type(parameters = numeric_list, required_type = "numeric", test_function = is.numeric)
   # Check character parameters.
   character_list <- list("group.by" = group.by,
@@ -82,6 +82,7 @@ do_CopyNumberVariantPlot <- function(sample,
   check_parameters(parameter = legend.position, parameter_name = "legend.position")
   check_parameters(parameter = viridis_color_map, parameter_name = "viridis_color_map")
   check_parameters(parameter = viridis_direction, parameter_name = "viridis_direction")
+  check_parameters(parameter = rotate_x_axis_labels, parameter_name = "rotate_x_axis_labels")
 
   if (is.null(chromosome_focus)){
     chromosome_list <- c(as.character(seq(1, 22)))

R/do_DotPlot.R

@@ -30,7 +30,7 @@ do_DotPlot <- function(sample,
                        legend.framecolor = "grey50",
                        legend.tickcolor = "white",
                        dot.scale = 6,
-                       colors.use = c("#1BFFFF", "#2E3192"),
+                       colors.use = c("#1BFFFF25", "#2E3192"),
                        plot.title = NULL,
                        plot.subtitle = NULL,
                        plot.caption = NULL,
@@ -40,7 +40,7 @@ do_DotPlot <- function(sample,
                        font.type = "sans",
                        cluster.idents = FALSE,
                        flip = FALSE,
-                       rotate_x_axis_labels = TRUE,
+                       rotate_x_axis_labels = 45,
                        scale.by = "size",
                        use_viridis = FALSE,
                        viridis_color_map = "G",
@@ -60,7 +60,6 @@ do_DotPlot <- function(sample,
     # Check logical parameters.
     logical_list <- list("flip" = flip,
                          "cluster.idents" = cluster.idents,
-                         "rotate_x_axis_labels" = rotate_x_axis_labels,
                          "use_viridis" = use_viridis,
                          "dot_border" = dot_border,
                          "plot.grid" = plot.grid)
@@ -72,7 +71,8 @@ do_DotPlot <- function(sample,
                          "legend.tickwidth" = legend.tickwidth,
                          "legend.length" = legend.length,
                          "legend.width" = legend.width,
-                         "viridis_direction" = viridis_direction)
+                         "viridis_direction" = viridis_direction,
+                         "rotate_x_axis_labels" = rotate_x_axis_labels)
     check_type(parameters = numeric_list, required_type = "numeric", test_function = is.numeric)
     # Check character parameters.
     character_list <- list("legend.position" = legend.position,
@@ -125,6 +125,7 @@ do_DotPlot <- function(sample,
     check_parameters(parameter = viridis_direction, parameter_name = "viridis_direction")
     check_parameters(parameter = viridis_color_map, parameter_name = "viridis_color_map")
     check_parameters(parameter = grid.type, parameter_name = "grid.type")
+    check_parameters(parameter = rotate_x_axis_labels, parameter_name = "rotate_x_axis_labels")
 
     # Check colors.
     check_colors(colors.use)
@@ -200,10 +201,11 @@ do_DotPlot <- function(sample,
          ggplot2::theme_minimal(base_size = font.size) +
          ggplot2::theme(axis.text.x = ggplot2::element_text(color = "black",
                                                             face = "bold",
-                                                            angle = ifelse(isTRUE(rotate_x_axis_labels), 45, 0),
-                                                            hjust = ifelse(isTRUE(rotate_x_axis_labels), 1, 0.5),
-                                                            vjust = ifelse(isTRUE(rotate_x_axis_labels), 1, 1)),
+                                                            angle = get_axis_parameters(angle = rotate_x_axis_labels, flip = flip)[["angle"]],
+                                                            hjust = get_axis_parameters(angle = rotate_x_axis_labels, flip = flip)[["hjust"]],
+                                                            vjust = get_axis_parameters(angle = rotate_x_axis_labels, flip = flip)[["vjust"]]),
                         axis.text.y = ggplot2::element_text(face = "bold", color = "black"),
+                        axis.ticks = ggplot2::element_line(color = "black"),
                         axis.line = ggplot2::element_line(color = "black"),
                         axis.title = ggplot2::element_text(face = "bold"),
                         plot.title = ggplot2::element_text(face = "bold", hjust = 0),

R/do_GeyserPlot.R

@@ -46,7 +46,7 @@ do_GeyserPlot <- function(sample,
                           legend.type = "colorbar",
                           font.size = 14,
                           font.type = "sans",
-                          rotate_x_axis_labels = TRUE,
+                          rotate_x_axis_labels = 45,
                           viridis_color_map = "G",
                           viridis_direction = 1,
                           colors.use = NULL,
@@ -60,7 +60,8 @@ do_GeyserPlot <- function(sample,
                           plot.subtitle = NULL,
                           plot.caption = NULL,
                           xlab = "Groups",
-                          ylab = feature){
+                          ylab = feature,
+                          flip = FALSE){
 
   check_suggests(function_name = "do_GeyserPlot")
   # Check if the sample provided is a Seurat object.
@@ -69,8 +70,8 @@ do_GeyserPlot <- function(sample,
   # Check logical parameters.
   logical_list <- list("enforce_symmetry" = enforce_symmetry,
                        "order_by_mean" = order_by_mean,
-                       "rotate_x_axis_labels" = rotate_x_axis_labels,
-                       "plot_cell_borders" = plot_cell_borders)
+                       "plot_cell_borders" = plot_cell_borders,
+                       "flip" = flip)
   check_type(parameters = logical_list, required_type = "logical", test_function = is.logical)
   # Check numeric parameters.
   numeric_list <- list("pt.size" = pt.size,
@@ -84,7 +85,8 @@ do_GeyserPlot <- function(sample,
                        "legend.ncol" = legend.ncol,
                        "legend.nrow" = legend.nrow,
                        "legend.icon.size" = legend.icon.size,
-                       "viridis_direction" = viridis_direction)
+                       "viridis_direction" = viridis_direction,
+                       "rotate_x_axis_labels" = rotate_x_axis_labels)
   check_type(parameters = numeric_list, required_type = "numeric", test_function = is.numeric)
   # Check character parameters.
 
@@ -119,6 +121,7 @@ do_GeyserPlot <- function(sample,
   check_parameters(parameter = viridis_direction, parameter_name = "viridis_direction")
   check_parameters(parameter = viridis_color_map, parameter_name = "viridis_color_map")
   check_parameters(parameter = scale_type, parameter_name = "scale_type")
+  check_parameters(parameter = rotate_x_axis_labels, parameter_name = "rotate_x_axis_labels")
 
   `%>%` <- magrittr::`%>%`
   # Check the assay.
@@ -364,12 +367,13 @@ do_GeyserPlot <- function(sample,
          ggplot2::theme_minimal(base_size = font.size) +
          ggplot2::theme(axis.title = ggplot2::element_text(color = "black",
                                                            face = "bold"),
-                        axis.line.x = ggplot2::element_line(color = "black"),
+                        axis.line.x = if (isFALSE(flip)) {ggplot2::element_line(color = "black")} else if (isTRUE(flip)) {ggplot2::element_blank()},
+                        axis.line.y = if (isTRUE(flip)) {ggplot2::element_line(color = "black")} else if (isFALSE(flip)) {ggplot2::element_blank()},
                         axis.text.x = ggplot2::element_text(color = "black",
                                                             face = "bold",
-                                                            angle = ifelse(isTRUE(rotate_x_axis_labels), 45, 0),
-                                                            hjust = ifelse(isTRUE(rotate_x_axis_labels), 1, 0.5),
-                                                            vjust = ifelse(isTRUE(rotate_x_axis_labels), 1, 1)),
+                                                            angle = get_axis_parameters(angle = rotate_x_axis_labels, flip = flip)[["angle"]],
+                                                            hjust = get_axis_parameters(angle = rotate_x_axis_labels, flip = flip)[["hjust"]],
+                                                            vjust = get_axis_parameters(angle = rotate_x_axis_labels, flip = flip)[["vjust"]]),
                         axis.text.y = ggplot2::element_text(color = "black", face = "bold"),
                         axis.ticks = ggplot2::element_line(color = "black"),
                         panel.grid.major = ggplot2::element_blank(),
@@ -420,5 +424,10 @@ do_GeyserPlot <- function(sample,
     }
     list.out[[feature]] <- p
   }
+
+  if (isTRUE(flip)){
+    p <- p +
+         ggplot2::coord_flip()
+  }
   return(if (length(features) > 1) {list.out} else {p})
 }