Function renamiming.

NAMESPACE

@@ -1,6 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
-export(do_AffinityAnalysisPlot)
+export(do_AffinityHeatmap)
 export(do_AlluvialPlot)
 export(do_BarPlot)
 export(do_BeeSwarmPlot)
@@ -16,20 +16,20 @@ export(do_EnrichmentHeatmap)
 export(do_ExpressionHeatmap)
 export(do_FeaturePlot)
 export(do_GeyserPlot)
-export(do_GroupwiseDEPlot)
+export(do_GroupwiseDEHeatmap)
 export(do_LigandReceptorPlot)
 export(do_LoadingsHeatmap)
 export(do_MetadataPlot)
 export(do_NebulosaPlot)
 export(do_PackageReport)
-export(do_PathwayActivityPlot)
+export(do_PathwayActivityHeatmap)
 export(do_RankedEnrichmentHeatmap)
 export(do_RankedExpressionHeatmap)
 export(do_RidgePlot)
 export(do_SCEnrichmentHeatmap)
 export(do_SCExpressionHeatmap)
 export(do_SavePlot)
-export(do_TFActivityPlot)
+export(do_TFActivityHeatmap)
 export(do_TermEnrichmentPlot)
 export(do_ViolinPlot)
 export(do_VolcanoPlot)

NEWS.md

@@ -1,7 +1,13 @@
-# SCpbur v2.0.3 (In Development)
+# SCpbur v3.0.0 (In Development)
+
+## Reason for the mejor version change
+-   Due to the preparation for the publication of SCpubr's manuscript, a major effort has been made to further standardize and wrap up the package nicely.
+-   Some functions have been removed, and many have been renamed, for consistency.
+-   Development versions have been transferred to the normal release, with the exception of `SCpubr::do_SavePlot()`.
 
 ## General
 -   Enhanced startup message for clarity. Not it guides the user to run `SCpubr::package_report(extended = TRUE)` to get an overview of the missing dependencies.
+-   Added black border to glyphs in legends.
 
 ## Added functions
 -   `do_WafflePlot()`: This function displays proportions as a pictogram grid of 10x10 tiles. It helps to visually see at a glance the proportions of your data. This fails to correctly convey decimal proportions and completely ignores heavily under-represented classes in your dataset. 
@@ -15,9 +21,13 @@ The reason behind it is that they, together with do_TermEnrichmentPlot() targete
 
 ## Renamed functions
 -   `do_DiffusionMapPlot()` is now called `do_RankedEnrichmentHeatmap()`. As it now accepts any dimensional reduction and not only diffusion maps.
--   `save_plot()` (development release only) is now called `do_SavePlot()`. This is a preparation for the version `2.0.3` which will launch together with the publication.
--   `package_report()`  is now called `do_PackageReport()`. This is a preparation for the version `2.0.3` which will launch together with the publication.
--   `do_LoadingsPlot()` is now called `do_LoadingsHeatmap()`. This is a preparation for the version `2.0.3` which will launch together with the publication.
+-   `save_plot()` (development release only) is now called `do_SavePlot()`. This is a preparation for the version `3.0.0` which will launch together with the publication.
+-   `package_report()`  is now called `do_PackageReport()`. This is a preparation for the version `3.0.0` which will launch together with the publication.
+-   `do_LoadingsPlot()` is now called `do_LoadingsHeatmap()`. This is a preparation for the version `3.0.0` which will launch together with the publication.
+-   `do_AffinityAnalysisPlot()` is now called `do_AffinityHeatmap()`. This is a preparation for the version `3.0.0` which will launch together with the publication.
+-   `do_PathwayActivityPlot()` is now called `do_PathwayActivityHeatmap()`. This is a preparation for the version `3.0.0` which will launch together with the publication.
+-   `do_TFActivityPlot()` is now called `do_TFActivityHeatmap()`. This is a preparation for the version `3.0.0` which will launch together with the publication.
+-   `do_GroupwiseDEPlot()` is now called `do_GroupwiseDEHeatmap()`. This is a preparation for the version `3.0.0` which will launch together with the publication.
 
 ## Heavily modified functions.
 -   `do_TermEnrichmentPlot()`: Recoded the whole function. Now accepts the result of using `clusterProfiler::enrichGO()`, `clusterProfiler::enrichKEGG()`, etc. The output is a dot plot with the terms on the Y axis, the Gene Ratio in the X, colored by the adjusted p-value and size mapped to the Gene Count.
@@ -26,6 +36,9 @@ The reason behind it is that they, together with do_TermEnrichmentPlot() targete
 
 The reason of these modification is to allow for a much clearer and concise output than before.
 
+## do_AffinityHeatmap()
+-   Changed legend title to "Z-Scored | ulm score", for consistency with other functions in the package.
+
 ## 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.
 -   Modified the legend items to have a black border.
@@ -58,7 +71,7 @@ The reason of these modification is to allow for a much clearer and concise outp
 -   Added `split.by.combined` parameter and set its default value to `TRUE`. This allows to toggle on or off whether to display the combined view when `split.by` is used.
 -   However, when `split.by`is used alongside `group.by`, it is now enforced to show the combined plot (`split.by.combined = TRUE`), to avoid bugs.
 -   Added `legend.dot.border` parameter to select whether we want a black border around the legend dots or not.
--   Fixed a bug in which `font.family` would not be applied when `label = TRUE`. [(#76)](https://github.com/enblacar/SCpubr/issues/76)
+-   Fixed a bug in which `font.family` would not be applied when `label = TRUE`. 
 
 ## do_DotPlot()
 -   Fixed a bug that caused sequential palettes to not be checked properly.
@@ -80,14 +93,27 @@ The reason of these modification is to allow for a much clearer and concise outp
 ## do_FeaturePlot()
 -   Fixed a bug in which legend titles would not show up as intended.
 -   Enabled the use of several legend titles when multiple features are provided. The number of legend titles and features have to be equal.
--   Fixed a bug in which `font.family` would not be applied when `label = TRUE`. [(#76)](https://github.com/enblacar/SCpubr/issues/76)
+-   Fixed a bug in which `font.family` would not be applied when `label = TRUE`. 
+-   Added `scale.limits` parameter to control the range of values the color scale should take. This is specially useful if you want to plot several features and make the color comparable between them. 
+
+## do_GroupwiseDEHeatmap()
+-   Reduced the legend title texts to allow for more room in the plot.
 
 ## do_LigandReceptorPlot()
 -   Added a new parameter `top_interactions_by_group` which when set to `TRUE` will report for each pair of `source` and `target`, as many interactions as stated in `top_interactions`.
 
+## do_PathwayActivityHeatmap
+-   Changed legend title to "Z-Scored | <statistic> score", for consistency with other functions in the package.
+
 ## do_RidgePlot()
 -   Removed `size = 1.25` aesthetic from the call to `ggridges::geom_ridge...`.
 
+## do_SavePlot()
+-   Added `limitsize` parameter, that allows for very big ggplot2-based plots to be saved with big dimensions.
+
+## do_TFActivityHeatmap()
+-   Changed legend title to "Z-Scored | <statistic> score", for consistency with other functions in the package.
+
 ## do_ViolinPlot()
 -   Added `order` parameter to reorder the groups based on the median. Only works when `split.by` is set to `NULL`.
 -   Fixed typos in error logging.

R/do_AffinityAnalysisPlot.R → R/do_AffinityHeatmap.R

@@ -11,58 +11,58 @@
 #' @return A list containing different plots.
 #' @export
 #'
-#' @example /man/examples/examples_do_AffinityAnalysisPlot.R
-
-do_AffinityAnalysisPlot <- function(sample,
-                                    input_gene_list,
-                                    subsample = 2500,
-                                    group.by = NULL,
-                                    assay = NULL,
-                                    slot = NULL,
-                                    statistic = "ulm",
-                                    number.breaks = 5,
-                                    use_viridis = FALSE,
-                                    viridis.palette = "G",
-                                    viridis.direction = -1,
-                                    sequential.palette = "YlGnBu",
-                                    sequential.direction = 1,
-                                    diverging.palette = "RdBu",
-                                    diverging.direction = -1,
-                                    enforce_symmetry = TRUE,
-                                    legend.position = "bottom",
-                                    legend.width = 1,
-                                    legend.length = 20,
-                                    legend.framewidth = 0.5,
-                                    legend.tickwidth = 0.5,
-                                    legend.framecolor = "grey50",
-                                    legend.tickcolor = "white",
-                                    legend.type = "colorbar",
-                                    na.value = "grey75",
-                                    font.size = 14,
-                                    font.type = "sans",
-                                    axis.text.x.angle = 45,
-                                    flip = FALSE,
-                                    colors.use = NULL,
-                                    min.cutoff = NA,
-                                    max.cutoff = NA,
-                                    verbose = TRUE,
-                                    return_object = FALSE,
-                                    grid.color = "white",
-                                    border.color = "black",
-                                    flavor = "Seurat",
-                                    nbin = 24,
-                                    ctrl = 100,
-                                    plot.title.face = "bold",
-                                    plot.subtitle.face = "plain",
-                                    plot.caption.face = "italic",
-                                    axis.title.face = "bold",
-                                    axis.text.face = "plain",
-                                    legend.title.face = "bold",
-                                    legend.text.face = "plain"){
+#' @example /man/examples/examples_do_AffinityHeatmap.R
+
+do_AffinityHeatmap <- function(sample,
+                               input_gene_list,
+                               subsample = 2500,
+                               group.by = NULL,
+                               assay = NULL,
+                               slot = NULL,
+                               statistic = "ulm",
+                               number.breaks = 5,
+                               use_viridis = FALSE,
+                               viridis.palette = "G",
+                               viridis.direction = -1,
+                               sequential.palette = "YlGnBu",
+                               sequential.direction = 1,
+                               diverging.palette = "RdBu",
+                               diverging.direction = -1,
+                               enforce_symmetry = TRUE,
+                               legend.position = "bottom",
+                               legend.width = 1,
+                               legend.length = 20,
+                               legend.framewidth = 0.5,
+                               legend.tickwidth = 0.5,
+                               legend.framecolor = "grey50",
+                               legend.tickcolor = "white",
+                               legend.type = "colorbar",
+                               na.value = "grey75",
+                               font.size = 14,
+                               font.type = "sans",
+                               axis.text.x.angle = 45,
+                               flip = FALSE,
+                               colors.use = NULL,
+                               min.cutoff = NA,
+                               max.cutoff = NA,
+                               verbose = TRUE,
+                               return_object = FALSE,
+                               grid.color = "white",
+                               border.color = "black",
+                               flavor = "Seurat",
+                               nbin = 24,
+                               ctrl = 100,
+                               plot.title.face = "bold",
+                               plot.subtitle.face = "plain",
+                               plot.caption.face = "italic",
+                               axis.title.face = "bold",
+                               axis.text.face = "plain",
+                               legend.title.face = "bold",
+                               legend.text.face = "plain"){
   # Add lengthy error messages.
   withr::local_options(.new = list("warning.length" = 8170))
 
-  check_suggests("do_AffinityAnalysisPlot")
+  check_suggests("do_AffinityHeatmap")
 
   check_Seurat(sample)
 
@@ -392,7 +392,7 @@ do_AffinityAnalysisPlot <- function(sample,
     p <- p +
          ggplot2::scale_fill_gradientn(colors = colors.gradient,
                                        na.value = na.value,
-                                       name = paste0(statistic, " | Scaled and Centered"),
+                                       name = paste0("Z-scored | ", statistic, " score"),
                                        breaks = scale.setup$breaks,
                                        labels = scale.setup$labels,
                                        limits = scale.setup$limits)

R/do_FeaturePlot.R

@@ -11,6 +11,7 @@
 #' @param group.by.colors.use \strong{\code{\link[base]{character}}} | Colors to use for the group dots.
 #' @param group.by.show.dots \strong{\code{\link[base]{logical}}} | Controls whether to place in the middle of the groups.
 #' @param group.by.cell_borders.alpha \strong{\code{\link[base]{numeric}}} | Controls the transparency of the new borders drawn by \strong{\code{group.by.cell_borders}}.
+#' @param scale.limits \strong{\code{\link[base]{numeric}}} | Vector of two values (i.e: \code{c(0, 1)}) to limit the scales. Particularly useful to extend the color scale beyond the values in the dataset, contrary to \code{min.cutoff} and \code{max.cutoff}. 
 #' @param symmetry.type \strong{\code{\link[base]{character}}} | Type of symmetry to be enforced. One of:
 #' \itemize{
 #'   \item \emph{\code{absolute}}: The highest absolute value will be taken into a account to generate the color scale. Works after \strong{\code{min.cutoff}} and \strong{\code{max.cutoff}}.
@@ -78,6 +79,7 @@ do_FeaturePlot <- function(sample,
                            plot.axes = FALSE,
                            min.cutoff = rep(NA, length(features)),
                            max.cutoff = rep(NA, length(features)),
+                           scale.limits = NULL,
                            plot_density_contour = FALSE,
                            contour.position = "bottom",
                            contour.color = "grey90",
@@ -249,6 +251,37 @@ do_FeaturePlot <- function(sample,
                                        crayon_body(" higher or equal than "),
                                        crayon_key("0"),
                                        crayon_body(".")))
+
+  if (!is.null(scale.limits)){
+    assertthat::assert_that(length(scale.limits) == 2,
+                            msg = paste0(add_cross(), crayon_body("Please provide a two values to "),
+                                         crayon_key("scale.limits"),
+                                         crayon_body(".")))
+  }
+
+
+  if (!is.null(scale.limits)){
+    comparison <- !is.na(min.cutoff)
+    for (item in comparison){
+      assertthat::assert_that(base::isFALSE(item),
+                              msg = paste0(add_cross(), crayon_body("When using "),
+                                           crayon_key("scale.limits"),
+                                           crayon_body(" you can not provide values to "),
+                                           crayon_key("min.cutoff"),
+                                           crayon_body(".")))
+    }
+
+    comparison <- !is.na(max.cutoff)
+    for (item in comparison){
+      assertthat::assert_that(base::isFALSE(item),
+                              msg = paste0(add_cross(), crayon_body("When using "),
+                                           crayon_key("scale.limits"),
+                                           crayon_body(" you can not provide values to "),
+                                           crayon_key("max.cutoff"),
+                                           crayon_body(".")))
+    }
+
+  }
 
 
   check_colors(border.color, parameter_name = "border.color")
@@ -421,6 +454,8 @@ do_FeaturePlot <- function(sample,
                                       assay = assay,
                                       reduction = NULL,
                                       slot = slot,
+                                      limits.use = scale.limits,
+                                      from_data = if (is.null(scale.limits)){FALSE} else {TRUE},
                                       number.breaks = number.breaks,
                                       min.cutoff = min.cutoff,
                                       max.cutoff = max.cutoff,
@@ -444,6 +479,8 @@ do_FeaturePlot <- function(sample,
                                       assay = assay,
                                       reduction = NULL,
                                       slot = slot,
+                                      limits.use = scale.limits,
+                                      from_data = if (is.null(scale.limits)){FALSE} else {TRUE},
                                       number.breaks = number.breaks,
                                       min.cutoff = min.cutoff[counter],
                                       max.cutoff = max.cutoff[counter],
@@ -677,6 +714,8 @@ do_FeaturePlot <- function(sample,
                                       assay = assay,
                                       reduction = NULL,
                                       slot = slot,
+                                      limits.use = scale.limits,
+                                      from_data = if (is.null(scale.limits)){FALSE} else {TRUE},
                                       number.breaks = number.breaks,
                                       min.cutoff = min.cutoff.use,
                                       max.cutoff = max.cutoff.use,
@@ -861,6 +900,8 @@ do_FeaturePlot <- function(sample,
                                         feature = feature,
                                         assay = assay,
                                         reduction = NULL,
+                                        limits.use = scale.limits,
+                                        from_data = if (is.null(scale.limits)){FALSE} else {TRUE},
                                         slot = slot,
                                         number.breaks = number.breaks,
                                         min.cutoff = min.cutoff.use,