update refactor

figures/S11/notebooks/S11.ipynb

@@ -17,15 +17,15 @@
    },
    "outputs": [],
    "source": [
-    "suppressWarnings(suppressPackageStartupMessages(library(ggplot2)))\n",
-    "suppressWarnings(suppressPackageStartupMessages(library(platetools)))\n",
-    "suppressWarnings(suppressPackageStartupMessages(library(gridExtra)))\n",
-    "suppressWarnings(suppressPackageStartupMessages(library(cowplot)))\n",
-    "suppressWarnings(suppressPackageStartupMessages(library(viridis)))\n",
-    "suppressWarnings(suppressPackageStartupMessages(library(argparse)))\n",
-    "suppressWarnings(suppressPackageStartupMessages(library(patchwork)))\n",
-    "suppressWarnings(suppressPackageStartupMessages(library(arrow)))\n",
-    "suppressWarnings(suppressPackageStartupMessages(library(dplyr)))"
+    "suppressWarnings(suppressPackageStartupMessages(library(ggplot2))) # plotting\n",
+    "suppressWarnings(suppressPackageStartupMessages(library(platetools))) # plotting\n",
+    "suppressWarnings(suppressPackageStartupMessages(library(gridExtra))) # plot assembly\n",
+    "suppressWarnings(suppressPackageStartupMessages(library(cowplot))) # plot assembly\n",
+    "suppressWarnings(suppressPackageStartupMessages(library(viridis))) # color palettes\n",
+    "suppressWarnings(suppressPackageStartupMessages(library(argparse))) # command line arguments\n",
+    "suppressWarnings(suppressPackageStartupMessages(library(patchwork))) # plot assembly\n",
+    "suppressWarnings(suppressPackageStartupMessages(library(arrow))) # reading parquet files\n",
+    "suppressWarnings(suppressPackageStartupMessages(library(dplyr))) # data manipulation"
    ]
   },
   {
@@ -338,15 +338,13 @@
    ],
    "source": [
     "# set path to the PBMC metadata file\n",
-    "metadata_file_path_PBMC <-file.path(\n",
+    "metadata_file_path_PBMC <- file.path(\n",
     "    \"..\",\n",
     "    \"..\",\n",
     "    \"..\",\n",
     "    \"data\",\n",
     "    \"PBMC_preprocessed_sc_norm.parquet\"\n",
     ")\n",
-    "# load the metadata file via arrow \n",
-    "# metadata_file <- arrow::read_parquet(metadata_file_path)\n",
     "\n",
     "# load via arrow with certain columns\n",
     "metadata_file_PBMC <- arrow::read_parquet(\n",
@@ -361,7 +359,7 @@
     "\n",
     "# SHSY5Y\n",
     "# set path to the SHSY5Y metadata file\n",
-    "metadata_file_path_SHSY5Y <-file.path(\n",
+    "metadata_file_path_SHSY5Y <- file.path(\n",
     "    \"..\",\n",
     "    \"..\",\n",
     "    \"..\",\n",
@@ -547,7 +545,7 @@
     "    replacement = \"pool\",\n",
     "    x = metadata_file_PBMC$label\n",
     ")\n",
-    "# aggreagate the metadata via Metadata_Well\n",
+    "# aggregate the metadata via Metadata_Well\n",
     "metadata_file_PBMC <- metadata_file_PBMC %>%\n",
     "    group_by(Metadata_Well, Metadata_cell_type, label) %>%\n",
     "    summarize(\n",
@@ -574,7 +572,7 @@
     "    replacement = \"pool\",\n",
     "    x = metadata_file_SHSY5Y$label\n",
     ")\n",
-    "# aggreagate the metadata via Metadata_Well\n",
+    "# aggregate the metadata via Metadata_Well\n",
     "metadata_file_SHSY5Y <- metadata_file_SHSY5Y %>%\n",
     "    group_by(Metadata_Well, Metadata_cell_type, label) %>%\n",
     "    summarize(\n",

figures/S11/scripts/S11.r

@@ -1,12 +1,12 @@
-suppressWarnings(suppressPackageStartupMessages(library(ggplot2)))
-suppressWarnings(suppressPackageStartupMessages(library(platetools)))
-suppressWarnings(suppressPackageStartupMessages(library(gridExtra)))
-suppressWarnings(suppressPackageStartupMessages(library(cowplot)))
-suppressWarnings(suppressPackageStartupMessages(library(viridis)))
-suppressWarnings(suppressPackageStartupMessages(library(argparse)))
-suppressWarnings(suppressPackageStartupMessages(library(patchwork)))
-suppressWarnings(suppressPackageStartupMessages(library(arrow)))
-suppressWarnings(suppressPackageStartupMessages(library(dplyr)))
+suppressWarnings(suppressPackageStartupMessages(library(ggplot2))) # plotting
+suppressWarnings(suppressPackageStartupMessages(library(platetools))) # plotting
+suppressWarnings(suppressPackageStartupMessages(library(gridExtra))) # plot assembly
+suppressWarnings(suppressPackageStartupMessages(library(cowplot))) # plot assembly
+suppressWarnings(suppressPackageStartupMessages(library(viridis))) # color palettes
+suppressWarnings(suppressPackageStartupMessages(library(argparse))) # command line arguments
+suppressWarnings(suppressPackageStartupMessages(library(patchwork))) # plot assembly
+suppressWarnings(suppressPackageStartupMessages(library(arrow))) # reading parquet files
+suppressWarnings(suppressPackageStartupMessages(library(dplyr))) # data manipulation
 
 # define the base directory
 base_dir <- file.path(
@@ -56,15 +56,13 @@ head(index_file_SHSY5Y,2)
 
 
 # set path to the PBMC metadata file
-metadata_file_path_PBMC <-file.path(
+metadata_file_path_PBMC <- file.path(
     "..",
     "..",
     "..",
     "data",
     "PBMC_preprocessed_sc_norm.parquet"
 )
-# load the metadata file via arrow
-# metadata_file <- arrow::read_parquet(metadata_file_path)
 
 # load via arrow with certain columns
 metadata_file_PBMC <- arrow::read_parquet(
@@ -79,7 +77,7 @@ head(metadata_file_PBMC)
 
 # SHSY5Y
 # set path to the SHSY5Y metadata file
-metadata_file_path_SHSY5Y <-file.path(
+metadata_file_path_SHSY5Y <- file.path(
     "..",
     "..",
     "..",
@@ -117,7 +115,7 @@ metadata_file_PBMC$label <- gsub(
     replacement = "pool",
     x = metadata_file_PBMC$label
 )
-# aggreagate the metadata via Metadata_Well
+# aggregate the metadata via Metadata_Well
 metadata_file_PBMC <- metadata_file_PBMC %>%
     group_by(Metadata_Well, Metadata_cell_type, label) %>%
     summarize(
@@ -144,7 +142,7 @@ metadata_file_SHSY5Y$label <- gsub(
     replacement = "pool",
     x = metadata_file_SHSY5Y$label
 )
-# aggreagate the metadata via Metadata_Well
+# aggregate the metadata via Metadata_Well
 metadata_file_SHSY5Y <- metadata_file_SHSY5Y %>%
     group_by(Metadata_Well, Metadata_cell_type, label) %>%
     summarize(