update the rd with the new point layer

YuLab-SMU · Apr 12, 2024 · 030a98b · 030a98b
1 parent 26dd2ac
commit 030a98b
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Showing 8 changed files with 106 additions and 31 deletions.
diff --git a/R/sc-dim.R b/R/sc-dim.R
@@ -12,7 +12,19 @@
 ##' \code{alpha} or (\code{shape} when geom = geom_point) can be set manually.
 ##' @param geom the function of geometric layer, default is sc_geom_point,
 ##' other geometric layer, such as geom_point also works.
-##' @param ... additional parameters pass to 'scattermore::geom_scattermore()'
+##' @param ... additional parameters pass to \code{geom_scattermore2()}.
+##' \itemize{
+##'     \item \code{bg_colour} the colour of background point, default is \code{NA}.
+##'      this character also can be set in \code{mappint}.
+##'     \item \code{gap_colour} the colour of gap background, default is \code{'white'}.
+##'     \item \code{bg_line_width} the line width of background point, 
+##'      default is \code{.3}.
+##'     \item \code{gap_line_width} the gap line width of background point, 
+##'      default is \code{.1}.
+##'     \item \code{alpha} the transparency of colour, default is 1.
+##'     \item \code{subset} subset the data frame which meet conditions to display.
+##'      this should be set in \code{mapping}.
+#'  }
 ##' @return dimension reduction plot
 ##' @seealso
 ##'  [geom_scattermore][scattermore::geom_scattermore]; 

diff --git a/R/sc-feature.R b/R/sc-feature.R
@@ -20,6 +20,18 @@
 ##' @param common.legend whether to use \code{facet_wrap} to display the multiple 
 ##' \code{features}, default is TRUE.
 ##' @param ... additional parameters pass to 'scattermore::geom_scattermore()'
+##' \itemize{
+##'     \item \code{bg_colour} the colour of background point, default is \code{NA}.
+##'      this character also can be set in \code{mappint}.
+##'     \item \code{gap_colour} the colour of gap background, default is \code{'white'}.
+##'     \item \code{bg_line_width} the line width of background point,
+##'      default is \code{.3}.
+##'     \item \code{gap_line_width} the gap line width of background point,
+##'      default is \code{.1}.
+##'     \item \code{alpha} the transparency of colour, default is 1.
+##'     \item \code{subset} subset the data frame which meet conditions to display.
+##'      this should be set in \code{mapping}.
+##'  }
 ##' @return dimension reduction plot colored by selected features
 ##' @importFrom ggplot2 theme
 ##' @importFrom ggplot2 theme_bw

diff --git a/R/sc-geom-point.R b/R/sc-geom-point.R
@@ -14,7 +14,7 @@
 ##' sc_geom_point()
 sc_geom_point <- function(mapping=NULL, ...){
     default_params <- list(mapping = mapping, 
-                        pointsize = 4,
+                        pointsize = 3,
                         pixels = c(700, 700)
                     )
     params <- modifyList(default_params, list(...))
@@ -34,12 +34,13 @@ sc_geom_point <- function(mapping=NULL, ...){
 #' passed to \code{\link[grid]{rasterGrob}}.
 #' @param pointsize Radius of rasterized point. Use ‘0’ for single pixels (fastest).
 #' @param pixels Vector with X and Y resolution of the raster, default \code{c(512,512)}.
-#' @param gap_colour colour between the background and top point point layer,
-#' default is \code{white}. 
+#' @param gap_colour colour of gap background between the bottom background 
+#' and top point point layer, default is \code{white}. 
+#' @param gap_alpha numeric the transparency of gap background colour, default is 1.
 #' @param bg_line_width numeric the line width of background point layer, 
 #' default is \code{0.3}.
 #' @param gap_line_width numeric the line width of gap between the background and 
-#' top point point layer, default is \code{.05}.
+#' top point point layer, default is \code{.1}.
 #' @param ... Other arguments passed on to \code{\link[ggplot2]{layer}}.
 #' @details
 #'  \itemize{
@@ -61,7 +62,7 @@ sc_geom_point <- function(mapping=NULL, ...){
 geom_scattermore2 <- function(mapping = NULL, data = NULL, stat = "identity", position = "identity", ...,
                              na.rm = FALSE, show.legend = NA, inherit.aes = TRUE,
                              interpolate = FALSE, pointsize = 0, pixels = c(512, 512),
-                             gap_colour = 'white', bg_line_width = .3, gap_line_width = .05){
+                             gap_colour = 'white', gap_alpha = 1, bg_line_width = .3, gap_line_width = .1){
   ggplot2::layer(
     data = data,
     mapping = mapping,
@@ -76,6 +77,7 @@ geom_scattermore2 <- function(mapping = NULL, data = NULL, stat = "identity", po
       pointsize = pointsize,
       pixels = pixels,
       gap_colour = gap_colour,
+      gap_alpha = gap_alpha,
       bg_line_width = bg_line_width,
       gap_line_width = gap_line_width,
       ...
@@ -104,8 +106,9 @@ GeomScattermore2 <- ggplot2::ggproto("GeomScattermore2", ggplot2::Geom,
                         na.rm = FALSE,
                         pixels = c(512, 512),
                         gap_colour = 'white',
+                        gap_alpha = 1,
                         bg_line_width = .3,
-                        gap_line_width = .05){
+                        gap_line_width = .1){
     coords <- coord$transform(data, pp)
 
     upperimage <- scattermore(cbind(coords$x, coords$y),
@@ -126,7 +129,7 @@ GeomScattermore2 <- ggplot2::ggproto("GeomScattermore2", ggplot2::Geom,
                                ylim = c(0, 1),
                                size = pixels)
         gapimage <- scattermore(cbind(coords$x, coords$y),
-                                rgba = grDevices::col2rgb(alpha = TRUE, scales::alpha(gap_colour, 1)),
+                                rgba = grDevices::col2rgb(alpha = TRUE, scales::alpha(gap_colour, gap_alpha)),
                                 cex = gapsize,
                                 xlim = c(0, 1),
                                 ylim = c(0, 1),

diff --git a/R/sc-spatial.R b/R/sc-spatial.R
@@ -30,8 +30,20 @@
 ##' default is prod.
 ##' @param common.legend whether to use \code{facet_wrap} to display the multiple
 ##' \code{features}, default is TRUE.
-##' @param point.size the size of point, default is 5.
-##' @param ... additional parameters.
+##' @param pointsize the size of point, default is 5.
+##' @param ... additional parameters, see also \code{geom_scattermore2()}.
+##' \itemize{
+##'     \item \code{bg_colour} the colour of background point, default is \code{NA}.
+##'      this character also can be set in \code{mappint}.
+##'     \item \code{gap_colour} the colour of gap background, default is \code{'white'}.
+##'     \item \code{bg_line_width} the line width of background point,
+##'      default is \code{.3}.
+##'     \item \code{gap_line_width} the gap line width of background point,
+##'      default is \code{.1}.
+##'     \item \code{alpha} the transparency of colour, default is 1.
+##'     \item \code{subset} subset the data frame which meet conditions to display.
+##'      this should be set in \code{mapping}.
+##'  }
 ##' @return ggplot object
 ##' @importFrom grid rasterGrob unit
 ##' @importFrom ggplot2 facet_grid annotation_custom
@@ -74,7 +86,7 @@ setGeneric('sc_spatial', function(object,
                                   joint = FALSE,
                                   joint.fun = prod,
                                   common.legend = TRUE,
-                                  point.size = 5,
+                                  pointsize = 5,
                                   ...) 
            standardGeneric('sc_spatial')
 )
@@ -90,7 +102,7 @@ setMethod("sc_spatial", 'Seurat',
                    image.rotate.degree = NULL, image.mirror.axis = 'v', 
                    remove.point = FALSE, mapping = NULL, ncol = 6, 
                    density=FALSE, grid.n = 100, joint = FALSE, 
-                   joint.fun = prod, common.legend = TRUE, point.size = 5, ...) {
+                   joint.fun = prod, common.legend = TRUE, pointsize = 5, ...) {
     images <- SeuratObject::Images(object = object, 
                     assay = Seurat::DefaultAssay(object = object)
                 )
@@ -145,7 +157,6 @@ setMethod("sc_spatial", 'Seurat',
         mapping <- default_mapping
     }
 
-    ratio <- .cal_ratio(d, mapping)
 
     if (!plot.pie){
         p <- ggplot(d, mapping)
@@ -162,7 +173,7 @@ setMethod("sc_spatial", 'Seurat',
     }
 
     if ((!remove.point && (!is.null(features) || (any(names(mapping) %in% c('color', 'colour')) && is.null(features))) && !plot.pie)){
-        p <- p + sc_geom_point(pointsize = point.size, ...)
+        p <- p + sc_geom_point(pointsize = pointsize, ...)
     }else if (!remove.point && plot.pie){
         rlang::check_installed('scatterpie', 'is required when `plot.pie=TRUE`')
         p <- p + scatterpie::geom_scatterpie(data=d, mapping=mapping, cols='features', long_format=TRUE, pie_scale=pie.radius.scale, ...)
@@ -174,7 +185,7 @@ setMethod("sc_spatial", 'Seurat',
          .feature_setting(features, ncol, plot.pie) +
          ylab(NULL) +
          xlab(NULL) +
-         coord_fixed(ratio=ratio) +
+         coord_fixed() +
          theme_bw2() 
 
     color.aes <- .check_aes_exits(p$mapping, c('color', 'colour'))
@@ -282,8 +293,6 @@ setMethod('sc_spatial', 'SingleCellExperiment', function(object,
         mapping <- default_mapping
     }
 
-    ratio <- .cal_ratio(d, mapping)
-
     if (!plot.pie){
         p <- ggplot(d, mapping)
     }else{
@@ -299,7 +308,7 @@ setMethod('sc_spatial', 'SingleCellExperiment', function(object,
     }
 
     if ((!remove.point && (!is.null(features) || (any(names(mapping) %in% c('color', 'colour')) && is.null(features))) && !plot.pie)){
-        p <- p + sc_geom_point(pointsize = point.size, ...) 
+        p <- p + sc_geom_point(pointsize = pointsize, ...) 
     }else if (!remove.point && plot.pie){
         rlang::check_installed('scatterpie', 'is required when `plot.pie=TRUE`')
         p <- p + scatterpie::geom_scatterpie(data=d, mapping=mapping, cols='features', long_format=TRUE, pie_scale = pie.radius.scale, ...)
@@ -311,7 +320,7 @@ setMethod('sc_spatial', 'SingleCellExperiment', function(object,
          .feature_setting(features, ncol, plot.pie) +
          ylab(NULL) +
          xlab(NULL) +
-         coord_fixed(ratio = ratio) +
+         coord_fixed() +
          theme_bw2() 
 
     color.aes <- .check_aes_exits(p$mapping, c('color', 'colour'))

diff --git a/man/geom_scattermore2.Rd b/man/geom_scattermore2.Rd
diff --git a/man/sc-dim-methods.Rd b/man/sc-dim-methods.Rd
diff --git a/man/sc-feature-methods.Rd b/man/sc-feature-methods.Rd
diff --git a/man/sc-spatial-methods.Rd b/man/sc-spatial-methods.Rd