Merge pull request #35 from boyiguo1/v1.3.1

V1.3.1

NEWS.md

@@ -1,12 +1,14 @@
 # escheR 1.3.1
 SIGNIFICANT USER-VISIBLE CHANGES
+
 * Add functions `add_fill_bin` and `add_ground_bin` to provide hexgon binning strategy to mitigate the overplotting of data points
 * Provide an example to use `add_fill_bin` and `add_ground_bin` with `make_escheR` to create hexgon binning plot
 
 
 
 # escheR 1.2.0
 SIGNIFICANT USER-VISIBLE CHANGES
+
 * Add generic functions to support `SingleCellExperiment` object by
   providing values to the argument `dimred`, and `data.frame` object
 * Modify the generic function `make_escheR.SpatialExperiment` to support 

R/add_fill_bin.R

@@ -1,5 +1,6 @@
 #' @param bins numeric vector giving number of bins in both vertical and
 #'             horizontal directions. Set to 30 by default.
+#' @param fun  function for summary. See more detail in \link[ggplot2]{stat_summary_hex}
 #'
 #' @rdname add_fill
 #' @export
@@ -9,6 +10,7 @@ add_fill_bin <- function(
     var,
     bins = 30,
     point_size = 2.8,
+    fun = sum,
     ...){
   p +
     stat_summary_hex(
@@ -17,7 +19,7 @@ add_fill_bin <- function(
       geom = "point",
       shape = 21,
       size = 2.8,
-      fun = sum,
+      fun = fun,
       bins = bins
     ) +
     scale_fill_gradient(name = var)

vignettes/more_than_visium.Rmd

@@ -69,6 +69,7 @@ make_escheR(
   scale_color_discrete(name = "Spatial Domains") +
   theme_minimal()
 ```
+
 > Note 1: The strategy of binning to avoid overplotting is previously proposed in [`schex`](https://www.bioconductor.org/packages/release/bioc/html/schex.html). While we provide an implementation in `escheR`, we would caution our users that the binning strategy could lead to intermixing of cluster memberships. In our implementation, the majority membership of the data points belonging to a bin is selected as the label of the bin. Users should use the binning strategy under their own discretion, and interpret the visualization carefully.
 
 > Note 2: `add_fill_bin()` shoudl be applied after `add_ground_bin()` for the better visualization outcome.