V01 Pipeline

LewisLabUCSD · Feb 17, 2022 · f573989 · f573989
1 parent d0881d0
commit f573989
Show file tree

Hide file tree

Showing 13 changed files with 45,772 additions and 962 deletions.
diff --git a/R_scripts/annotation_clones/addClones.v01.vCurrent.ipynb b/R_scripts/annotation_clones/addClones.v01.vCurrent.ipynb
@@ -417,111 +417,6 @@
     "donors"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "b567b90b",
-   "metadata": {
-    "scrolled": true
-   },
-   "outputs": [],
-   "source": [
-    "dimplots.f <- function(cl, se){\n",
-    "    print(cl)\n",
-    "    d <- (DimPlot(object = subset(x = se, subset = name == cl), label = FALSE, \n",
-    "                   split.by=c(\"donor\"), group.by=(\"seurat_clusters\")))\n",
-    "    ggsave(file.path(clone.umap.condition.splitdonor, paste0(\"clone_\", cl, \".umap.png\")))\n",
-    "\n",
-    "}\n",
-    "\n",
-    "clone.umap.condition.splitdonor <- file.path(clone.umap.condition, \"clone_splitbydonor\")\n",
-    "dir.create(clone.umap.condition.splitdonor)\n",
-    "dimplots <- sapply(levels(se$name), FUN=dimplots.f, se=se)\n",
-    "\n",
-    "  "
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "b10aa2a7",
-   "metadata": {
-    "scrolled": true
-   },
-   "outputs": [],
-   "source": [
-    "  \n",
-    "# dimplots.alldon.f <- function(cl, se){\n",
-    "#     print(cl)\n",
-    "#     d <- (DimPlot(object = subset(x = se, subset = lineage == cl), label = FALSE, \n",
-    "#                    group.by=(\"seurat_clusters\"), split.by=\"condition\"))\n",
-    "#     ggsave(file.path(clone.umap.condition.alldonors, paste0(\"clone_\", cl, \".alldonors.umap.png\")))\n",
-    "\n",
-    "# }\n",
-    "\n",
-    "# clone.umap.condition.alldonors <- file.path(clone.umap.condition, \"alldonors\")\n",
-    "# dir.create(clone.umap.condition.alldonors)\n",
-    "\n",
-    "# dimplots <- sapply(levels(se$lineage), FUN=dimplots.alldon.f, se=se)\n",
-    "\n",
-    "\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "f49804d0",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "c4f72de2",
-   "metadata": {
-    "scrolled": true
-   },
-   "outputs": [],
-   "source": [
-    "dimplots.conditon.f <- function(cl, se){\n",
-    "    print(cl)\n",
-    "    d <- (DimPlot(object = subset(x = se, subset = name == cl), label = FALSE, \n",
-    "                   group.by=c(\"seurat_clusters\", \"donor\"), split.by=c(\"condition\")))\n",
-    "    ggsave(file.path(clone.umap.condition.lineage, paste0(\"clone_\", cl, \".condition.donors.umap.png\")))\n",
-    "}\n",
-    "\n",
-    "clone.umap.condition.lineage <- file.path(clone.umap.condition, \"lineage_condition\")\n",
-    "dir.create(clone.umap.condition.lineage)\n",
-    "\n",
-    "dimplots <- sapply(levels(se$name), FUN=dimplots.conditon.f, se=se)\n",
-    "\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "83b15064",
-   "metadata": {
-    "scrolled": true
-   },
-   "outputs": [],
-   "source": [
-    "# dimplots.donor.condition.f <- function(nm, se){\n",
-    "#     print(nm)\n",
-    "#     try({\n",
-    "#     d <- (DimPlot(object = subset(x = se, subset = (name == nm)), label = FALSE, \n",
-    "#                    group.by=\"seurat_clusters\", split.by=\"condition\"))\n",
-    "#     ggsave(file.path(donor.clone.umap.condition, paste0(\"donor_clone_\", nm, \".umap.png\")), d)\n",
-    "#     })\n",
-    "# }\n",
-    "\n",
-    "# donor.clone.umap.condition <- file.path(clone.umap.condition, \"donor_clone\")\n",
-    "# dir.create(donor.clone.umap.condition)\n",
-    "# dimplots <- sapply(levels(se$name), FUN=dimplots.donor.condition.f, se=se)\n",
-    "\n"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,

diff --git a/R_scripts/annotation_clones/input_donor_distribution.ipynb b/R_scripts/annotation_clones/input_donor_distribution.ipynb
diff --git a/R_scripts/annotation_clones/mtVarsPlot.ipynb b/R_scripts/annotation_clones/mtVarsPlot.ipynb