Rviz_update2

bioinfo-ucsd · Sep 13, 2024 · 95ce480 · 95ce480
1 parent d14487b
commit 95ce480
Showing 1 changed file with 16 additions and 60 deletions.
diff --git a/modules/06-dataviz/R_viz.ipynb b/modules/06-dataviz/R_viz.ipynb
@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 17,
+   "execution_count": 66,
    "id": "earned-theology",
    "metadata": {
     "vscode": {
@@ -26,7 +26,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 18,
+   "execution_count": 67,
    "id": "executive-hearing",
    "metadata": {
     "vscode": {
@@ -121,7 +121,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 19,
+   "execution_count": 68,
    "id": "protecting-associate",
    "metadata": {
     "vscode": {
@@ -153,7 +153,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 20,
+   "execution_count": 69,
    "id": "resistant-marketplace",
    "metadata": {
     "vscode": {
@@ -195,7 +195,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 21,
+   "execution_count": 70,
    "id": "postal-confidence",
    "metadata": {
     "vscode": {
@@ -238,7 +238,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 22,
+   "execution_count": 71,
    "id": "dangerous-defeat",
    "metadata": {
     "vscode": {
@@ -271,7 +271,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 23,
+   "execution_count": 72,
    "id": "immediate-infrared",
    "metadata": {
     "vscode": {
@@ -343,7 +343,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 24,
+   "execution_count": 73,
    "id": "worst-turner",
    "metadata": {
     "vscode": {
@@ -384,7 +384,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 25,
+   "execution_count": 74,
    "id": "frank-holmes",
    "metadata": {
     "vscode": {
@@ -433,7 +433,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 26,
+   "execution_count": 75,
    "id": "developed-carnival",
    "metadata": {
     "vscode": {
@@ -487,7 +487,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 27,
+   "execution_count": 76,
    "id": "removed-stroke",
    "metadata": {
     "vscode": {
@@ -547,7 +547,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 28,
+   "execution_count": 77,
    "id": "continued-elite",
    "metadata": {
     "vscode": {
@@ -760,7 +760,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 29,
+   "execution_count": 78,
    "id": "accomplished-pension",
    "metadata": {
     "vscode": {
@@ -786,7 +786,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 30,
+   "execution_count": 79,
    "id": "billion-victorian",
    "metadata": {
     "vscode": {
@@ -1000,52 +1000,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 31,
-   "id": "attractive-hygiene",
-   "metadata": {
-    "vscode": {
-     "languageId": "r"
-    }
-   },
-   "outputs": [],
-   "source": [
-    "# https://stackoverflow.com/questions/35717353/split-violin-plot-with-ggplot2\n",
-    "GeomSplitViolin <- ggproto(\"GeomSplitViolin\", GeomViolin, \n",
-    "                           draw_group = function(self, data, ..., draw_quantiles = NULL) {\n",
-    "  data <- transform(data, xminv = x - violinwidth * (x - xmin), xmaxv = x + violinwidth * (xmax - x))\n",
-    "  grp <- data[1, \"group\"]\n",
-    "  newdata <- plyr::arrange(transform(data, x = if (grp %% 2 == 1) xminv else xmaxv), if (grp %% 2 == 1) y else -y)\n",
-    "  newdata <- rbind(newdata[1, ], newdata, newdata[nrow(newdata), ], newdata[1, ])\n",
-    "  newdata[c(1, nrow(newdata) - 1, nrow(newdata)), \"x\"] <- round(newdata[1, \"x\"])\n",
-    "\n",
-    "  if (length(draw_quantiles) > 0 & !scales::zero_range(range(data$y))) {\n",
-    "    stopifnot(all(draw_quantiles >= 0), all(draw_quantiles <=\n",
-    "      1))\n",
-    "    quantiles <- ggplot2:::create_quantile_segment_frame(data, draw_quantiles)\n",
-    "    aesthetics <- data[rep(1, nrow(quantiles)), setdiff(names(data), c(\"x\", \"y\")), drop = FALSE]\n",
-    "    aesthetics$alpha <- rep(1, nrow(quantiles))\n",
-    "    both <- cbind(quantiles, aesthetics)\n",
-    "    quantile_grob <- GeomPath$draw_panel(both, ...)\n",
-    "    ggplot2:::ggname(\"geom_split_violin\", grid::grobTree(GeomPolygon$draw_panel(newdata, ...), quantile_grob))\n",
-    "  }\n",
-    "  else {\n",
-    "    ggplot2:::ggname(\"geom_split_violin\", GeomPolygon$draw_panel(newdata, ...))\n",
-    "  }\n",
-    "})\n",
-    "\n",
-    "geom_split_violin <- function(mapping = NULL, data = NULL, stat = \"ydensity\", position = \"identity\", ..., \n",
-    "                              draw_quantiles = NULL, trim = TRUE, scale = \"area\", na.rm = FALSE, \n",
-    "                              show.legend = NA, inherit.aes = TRUE) {\n",
-    "  layer(data = data, mapping = mapping, stat = stat, geom = GeomSplitViolin, \n",
-    "        position = position, show.legend = show.legend, inherit.aes = inherit.aes, \n",
-    "        params = list(trim = trim, scale = scale, draw_quantiles = draw_quantiles, na.rm = na.rm, ...))\n",
-    "}"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 32,
-   "id": "eleven-legend",
+   "execution_count": 80,
+   "id": "607b857b",
    "metadata": {
     "vscode": {
      "languageId": "r"