Merge pull request #18 from mjz1/dev

Dev

Author: mjz1

R/plotting.R

@@ -645,15 +645,15 @@ get_label_centers <- function(obj, group_var = "clusters", reduced_dim = "UMAP")
   # To any scatter of a umap can add + geom_label_repel(data = get_label_centers(sce), aes(x = x, y = y, label = clusters))
 
   if (class(obj) %in% c("SingleCellExperiment", "Milo")) {
-    x_means <- lapply(split(reducedDim(obj, reduced_dim)[, 1], obj[[group_var]]), mean) %>% unlist()
-    y_means <- lapply(split(reducedDim(obj, reduced_dim)[, 2], obj[[group_var]]), mean) %>% unlist()
+    x_means <- lapply(split(reducedDim(obj, reduced_dim)[, 1], obj[[group_var]]), median) %>% unlist()
+    y_means <- lapply(split(reducedDim(obj, reduced_dim)[, 2], obj[[group_var]]), median) %>% unlist()
     centers <- data.frame(x = x_means, y = y_means)
     centers[[group_var]] <- rownames(centers)
   }
 
   if ("Seurat" %in% class(obj)) {
-    x_means <- lapply(split(Seurat::Embeddings(obj, reduced_dim)[, 1], obj[[group_var]]), mean) %>% unlist()
-    y_means <- lapply(split(Seurat::Embeddings(obj, reduced_dim)[, 2], obj[[group_var]]), mean) %>% unlist()
+    x_means <- lapply(split(Seurat::Embeddings(obj, reduced_dim)[, 1], obj[[group_var]]), median) %>% unlist()
+    y_means <- lapply(split(Seurat::Embeddings(obj, reduced_dim)[, 2], obj[[group_var]]), median) %>% unlist()
     centers <- data.frame(x = x_means, y = y_means)
     centers[[group_var]] <- rownames(centers)
   }

renv.lock

@@ -3026,18 +3026,11 @@
     },
     "renv": {
       "Package": "renv",
-      "Version": "1.0.7.9000",
-      "Source": "GitHub",
-      "RemoteType": "github",
-      "RemoteUsername": "rstudio",
-      "RemoteRepo": "renv",
-      "RemoteRef": "main",
-      "RemoteSha": "8c2379948cb5667f47047b0e709c889fd2188feb",
-      "RemoteHost": "api.github.com",
-      "Requirements": [
-        "utils"
-      ],
-      "Hash": "73e0d7fbfb3035ae18fa10a9a923a40a"
+      "Version": "1.0.9",
+      "OS_type": null,
+      "NeedsCompilation": "no",
+      "Repository": "CRAN",
+      "Source": "Repository"
     },
     "reshape2": {
       "Package": "reshape2",

renv/activate.R

@@ -2,8 +2,8 @@
 local({
 
   # the requested version of renv
-  version <- "1.0.7.9000"
-  attr(version, "sha") <- "8c2379948cb5667f47047b0e709c889fd2188feb"
+  version <- "1.0.9"
+  attr(version, "sha") <- NULL
 
   # the project directory
   project <- Sys.getenv("RENV_PROJECT")
@@ -98,6 +98,66 @@ local({
     unloadNamespace("renv")
 
   # load bootstrap tools   
+  ansify <- function(text) {
+    if (renv_ansify_enabled())
+      renv_ansify_enhanced(text)
+    else
+      renv_ansify_default(text)
+  }
+  
+  renv_ansify_enabled <- function() {
+  
+    override <- Sys.getenv("RENV_ANSIFY_ENABLED", unset = NA)
+    if (!is.na(override))
+      return(as.logical(override))
+  
+    pane <- Sys.getenv("RSTUDIO_CHILD_PROCESS_PANE", unset = NA)
+    if (identical(pane, "build"))
+      return(FALSE)
+  
+    testthat <- Sys.getenv("TESTTHAT", unset = "false")
+    if (tolower(testthat) %in% "true")
+      return(FALSE)
+  
+    iderun <- Sys.getenv("R_CLI_HAS_HYPERLINK_IDE_RUN", unset = "false")
+    if (tolower(iderun) %in% "false")
+      return(FALSE)
+  
+    TRUE
+  
+  }
+  
+  renv_ansify_default <- function(text) {
+    text
+  }
+  
+  renv_ansify_enhanced <- function(text) {
+  
+    # R help links
+    pattern <- "`\\?(renv::(?:[^`])+)`"
+    replacement <- "`\033]8;;ide:help:\\1\a?\\1\033]8;;\a`"
+    text <- gsub(pattern, replacement, text, perl = TRUE)
+  
+    # runnable code
+    pattern <- "`(renv::(?:[^`])+)`"
+    replacement <- "`\033]8;;ide:run:\\1\a\\1\033]8;;\a`"
+    text <- gsub(pattern, replacement, text, perl = TRUE)
+  
+    # return ansified text
+    text
+  
+  }
+  
+  renv_ansify_init <- function() {
+  
+    envir <- renv_envir_self()
+    if (renv_ansify_enabled())
+      assign("ansify", renv_ansify_enhanced, envir = envir)
+    else
+      assign("ansify", renv_ansify_default, envir = envir)
+  
+  }
+  
   `%||%` <- function(x, y) {
     if (is.null(x)) y else x
   }
@@ -142,7 +202,10 @@ local({
     # compute common indent
     indent <- regexpr("[^[:space:]]", lines)
     common <- min(setdiff(indent, -1L)) - leave
-    paste(substring(lines, common), collapse = "\n")
+    text <- paste(substring(lines, common), collapse = "\n")
+  
+    # substitute in ANSI links for executable renv code
+    ansify(text)
 
   }