use air formatting

Author: schochastics

.Rbuildignore

@@ -29,4 +29,6 @@ paper.bib
 ^_quarto\.yml$
 ^\.quarto$
 ^methodshub
-.quarto/
+.quarto/
+^[\.]?air\.toml$
+^\.vscode$

.vscode/extensions.json

@@ -0,0 +1,5 @@
+{
+    "recommendations": [
+        "Posit.air-vscode"
+    ]
+}

.vscode/settings.json

@@ -0,0 +1,6 @@
+{
+    "[r]": {
+        "editor.formatOnSave": true,
+        "editor.defaultFormatter": "Posit.air-vscode"
+    }
+}

R/annotate_functions.R

@@ -22,31 +22,41 @@
 #'
 
 draw_circle <- function(col = "#00BFFF", use = "focus", max.circle) {
-    if (!requireNamespace("ggplot2", quietly = TRUE)) {
-        stop("ggplot2 needed for this function to work. Please install it.", call. = FALSE)
-    }
-    if (!use %in% c("focus", "cent")) {
-        stop("use must be one of 'focus' or 'cent'")
-    }
-    if (use == "focus" && missing(max.circle)) {
-        stop("max.circle missing. Should be set to the max distance from focal node.")
+  if (!requireNamespace("ggplot2", quietly = TRUE)) {
+    stop(
+      "ggplot2 needed for this function to work. Please install it.",
+      call. = FALSE
+    )
+  }
+  if (!use %in% c("focus", "cent")) {
+    stop("use must be one of 'focus' or 'cent'")
+  }
+  if (use == "focus" && missing(max.circle)) {
+    stop(
+      "max.circle missing. Should be set to the max distance from focal node."
+    )
+  }
+  dat <- data.frame()
+  if (use == "cent") {
+    for (d in seq(0, 100, 20) * 2) {
+      tmp <- as.data.frame(circleFun(center = c(0, 0), diameter = d))
+      tmp[["grp"]] <- d
+      dat <- rbind(dat, tmp)
     }
-    dat <- data.frame()
-    if (use == "cent") {
-        for (d in seq(0, 100, 20) * 2) {
-            tmp <- as.data.frame(circleFun(center = c(0, 0), diameter = d))
-            tmp[["grp"]] <- d
-            dat <- rbind(dat, tmp)
-        }
-    } else if (use == "focus") {
-        for (d in 1:max.circle) {
-            tmp <- as.data.frame(circleFun(center = c(0, 0), diameter = 2 * d))
-            tmp[["grp"]] <- d
-            dat <- rbind(dat, tmp)
-        }
+  } else if (use == "focus") {
+    for (d in 1:max.circle) {
+      tmp <- as.data.frame(circleFun(center = c(0, 0), diameter = 2 * d))
+      tmp[["grp"]] <- d
+      dat <- rbind(dat, tmp)
     }
-    circs <- ggplot2::geom_path(data = dat, ggplot2::aes_(x = ~x, y = ~y, group = ~grp), col = col, alpha = 0.5)
-    return(circs)
+  }
+  circs <- ggplot2::geom_path(
+    data = dat,
+    ggplot2::aes_(x = ~x, y = ~y, group = ~grp),
+    col = col,
+    alpha = 0.5
+  )
+  return(circs)
 }
 
 
@@ -75,48 +85,68 @@ draw_circle <- function(col = "#00BFFF", use = "focus", max.circle) {
 #' }
 #' @export
 #'
-annotate_circle <- function(cent, col = "#00BFFF", format = "", pos = "top", text_size = 3) {
-    if (!requireNamespace("ggplot2", quietly = TRUE)) {
-        stop("ggplot2 needed for this function to work. Please install it.", call. = FALSE)
-    }
-    if (length(cent) == 1) {
-        cent <- seq(1, cent, 1)
-        dat_annot <- data.frame(y = seq(0, 100, 20), x = 0, val = interpolate_cent(cent, seq(0, 100, 20)))
-        dat_annot[["val"]] <- round(dat_annot[["val"]], 8)
-    } else {
-        dat_annot <- data.frame(y = 100 - seq(0, 100, 20), x = 0, val = interpolate_cent(cent, seq(0, 100, 20)))
-        dat_annot[["val"]] <- round(dat_annot[["val"]], 8)
-    }
-    vju <- 0
-    if (format == "scientific") {
-        dat_annot[["val"]] <- format(dat_annot[["val"]], scientific = TRUE)
-    }
-    if (pos == "bottom") {
-        dat_annot[["y"]] <- -dat_annot[["y"]]
-        vju <- 1
-    }
-
-    circs <- ggplot2::geom_text(
-        data = dat_annot, ggplot2::aes_(x = ~x, y = ~y, label = ~val),
-        col = col, vjust = vju, size = text_size
+annotate_circle <- function(
+  cent,
+  col = "#00BFFF",
+  format = "",
+  pos = "top",
+  text_size = 3
+) {
+  if (!requireNamespace("ggplot2", quietly = TRUE)) {
+    stop(
+      "ggplot2 needed for this function to work. Please install it.",
+      call. = FALSE
     )
-    return(circs)
+  }
+  if (length(cent) == 1) {
+    cent <- seq(1, cent, 1)
+    dat_annot <- data.frame(
+      y = seq(0, 100, 20),
+      x = 0,
+      val = interpolate_cent(cent, seq(0, 100, 20))
+    )
+    dat_annot[["val"]] <- round(dat_annot[["val"]], 8)
+  } else {
+    dat_annot <- data.frame(
+      y = 100 - seq(0, 100, 20),
+      x = 0,
+      val = interpolate_cent(cent, seq(0, 100, 20))
+    )
+    dat_annot[["val"]] <- round(dat_annot[["val"]], 8)
+  }
+  vju <- 0
+  if (format == "scientific") {
+    dat_annot[["val"]] <- format(dat_annot[["val"]], scientific = TRUE)
+  }
+  if (pos == "bottom") {
+    dat_annot[["y"]] <- -dat_annot[["y"]]
+    vju <- 1
+  }
+
+  circs <- ggplot2::geom_text(
+    data = dat_annot,
+    ggplot2::aes_(x = ~x, y = ~y, label = ~val),
+    col = col,
+    vjust = vju,
+    size = text_size
+  )
+  return(circs)
 }
 
 
 # helper -----
 circleFun <- function(center = c(0, 0), diameter = 1, npoints = 100) {
-    r <- diameter / 2
-    tt <- seq(0, 2 * pi, length.out = npoints)
-    xx <- center[1] + r * cos(tt)
-    yy <- center[2] + r * sin(tt)
-    return(data.frame(x = xx, y = yy))
+  r <- diameter / 2
+  tt <- seq(0, 2 * pi, length.out = npoints)
+  xx <- center[1] + r * cos(tt)
+  yy <- center[2] + r * sin(tt)
+  return(data.frame(x = xx, y = yy))
 }
 
 interpolate_cent <- function(cent, x) {
-    a <- min(cent)
-    b <- max(cent)
-    alpha <- 100 / (b - a)
-    beta <- -100 / (b - a) * a
-    (x - beta) / alpha
+  a <- min(cent)
+  b <- max(cent)
+  alpha <- 100 / (b - a)
+  beta <- -100 / (b - a) * a
+  (x - beta) / alpha
 }

R/graph_manipulate.R

@@ -23,21 +23,21 @@ NULL
 #' @export
 
 reorder_edges <- function(g, attr, desc = TRUE) {
-    if (!"name" %in% igraph::vertex_attr_names(g)) {
-        igraph::V(g)$name <- 1:igraph::vcount(g)
-    }
-    edges_df <- igraph::as_data_frame(g, what = "edges")
-    edges_df <- edges_df[order(edges_df[[attr]], decreasing = desc), ]
+  if (!"name" %in% igraph::vertex_attr_names(g)) {
+    igraph::V(g)$name <- 1:igraph::vcount(g)
+  }
+  edges_df <- igraph::as_data_frame(g, what = "edges")
+  edges_df <- edges_df[order(edges_df[[attr]], decreasing = desc), ]
 
-    vertices <- igraph::as_data_frame(g, what = "vertices")
-    vattrs <- igraph::vertex_attr_names(g)
-    idname <- which(vattrs == "name")
-    vertices <- vertices[, c(idname, setdiff(seq_along(vattrs), idname))]
+  vertices <- igraph::as_data_frame(g, what = "vertices")
+  vattrs <- igraph::vertex_attr_names(g)
+  idname <- which(vattrs == "name")
+  vertices <- vertices[, c(idname, setdiff(seq_along(vattrs), idname))]
 
-    gn <- igraph::graph_from_data_frame(
-        d = edges_df,
-        directed = igraph::is_directed(g),
-        vertices = vertices
-    )
-    gn
+  gn <- igraph::graph_from_data_frame(
+    d = edges_df,
+    directed = igraph::is_directed(g),
+    vertices = vertices
+  )
+  gn
 }