update egret

Author: marouenbg

netbooks/netZooR/egret_banovich_netbook.ipynb

@@ -84,7 +84,6 @@
     "library(ggpubr)\n",
     "library(reshape2)\n",
     "library(jcolors)\n",
-    "library(ALPACA)\n",
     "library(gridExtra)\n",
     "library(extrafont)\n",
     "library(grid)\n",
@@ -115,7 +114,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "\n",
     "load(paste0(ppath,\"data/networks/finalEgret_v1_banovich_LCL_allModels_smart1_07032020_1_panda.RData\"))\n",
     "net <- melt(regnet)\n",
     "colnames(net) = c(\"tf\",\"gene\",\"score\")\n",
@@ -489,10 +487,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "\n",
     "indivs_high_erg_disrup <- cad_tfs_degree_hard_thresh_melted[which((cad_tfs_degree_hard_thresh_melted$tf_diff_degree>3) & (cad_tfs_degree_hard_thresh_melted$cellType == \"CM\")),]\n",
-    "indivs_high_erg_disrup\n",
-    "\n"
+    "indivs_high_erg_disrup"
    ]
   },
   {
@@ -504,22 +500,12 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
-   "metadata": {},
-   "outputs": [
-    {
-     "ename": "ERROR",
-     "evalue": "Error in eval(expr, envir, enclos): object 'cad_tfs_degree_hard_thresh_melted' not found\n",
-     "output_type": "error",
-     "traceback": [
-      "Error in eval(expr, envir, enclos): object 'cad_tfs_degree_hard_thresh_melted' not found\nTraceback:\n"
-     ]
-    }
-   ],
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
    "source": [
     "top_indiv <- cad_tfs_degree_hard_thresh_melted[which((cad_tfs_degree_hard_thresh_melted$tf_diff_degree== max(cad_tfs_degree_hard_thresh_melted$tf_diff_degree)) & (cad_tfs_degree_hard_thresh_melted$cellType == \"CM\")),]\n",
     "\n",
-    "\n",
     "# get tf disruption scores for ERG for all individuals in iPSC-CMs\n",
     "tf_disrup_erg_cm <- cad_tfs_degree_hard_thresh_melted[which((cad_tfs_degree_hard_thresh_melted$tf == \"ERG\") & (cad_tfs_degree_hard_thresh_melted$cellType == \"CM\")),c('indiv','tf_diff_degree')]"
    ]
@@ -638,8 +624,7 @@
     "merged_alpaca_table_qq <- cbind(merged_alpaca_table[,c(1)],as.data.frame(normalize.quantiles(as.matrix(merged_alpaca_table[,c(2:358)]))))\n",
     "colnames(merged_alpaca_table_qq) <- colnames(merged_alpaca_table)\n",
     "merged_alpaca_table_qq_sc <- cbind(merged_alpaca_table_qq[,c(1)],as.data.frame(t(scale(t(merged_alpaca_table_qq[,c(2:358)]), center = TRUE, scale = TRUE))))\n",
-    "colnames(merged_alpaca_table_qq_sc)[1] <- \"node\"\n",
-    "\n"
+    "colnames(merged_alpaca_table_qq_sc)[1] <- \"node\""
    ]
   },
   {
@@ -854,7 +839,7 @@
     "k <- k+1\n",
     "}\n",
     "\n",
-    "grid.draw(g)\n"
+    "grid.draw(g)"
    ]
   },
   {
@@ -877,13 +862,6 @@
     "\n",
     "[7] Padi, Megha, and John Quackenbush. \"Detecting phenotype-driven transitions in regulatory network structure.\" NPJ systems biology and applications 4.1 (2018): 1-12."
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {