Merge pull request WayScience#129 from MikeLippincott/refactor_figures

Refactor figures
MikeLippincott · Mar 5, 2024 · 257bc5f · 257bc5f
2 parents dffbf88 + c23cd9e
commit 257bc5f
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diff --git a/...1/2023_Cell_Death_Phenotypes_Figure 1.png → figures/1.figure1/figure1.png b/...1/2023_Cell_Death_Phenotypes_Figure 1.png → figures/1.figure1/figure1.png
diff --git a/figures/biblio_figure/data/README.md → figures/S1/data/README.md b/figures/biblio_figure/data/README.md → figures/S1/data/README.md
diff --git a/.../biblio_figure/data/apoptosis_results.csv → figures/S1/data/apoptosis_results.csv b/.../biblio_figure/data/apoptosis_results.csv → figures/S1/data/apoptosis_results.csv
diff --git a/.../biblio_figure/data/autophagy_results.csv → figures/S1/data/autophagy_results.csv b/.../biblio_figure/data/autophagy_results.csv → figures/S1/data/autophagy_results.csv
diff --git a/...iblio_figure/data/ferroptosis_results.csv → figures/S1/data/ferroptosis_results.csv b/...iblio_figure/data/ferroptosis_results.csv → figures/S1/data/ferroptosis_results.csv
diff --git a/...s/biblio_figure/data/necrosis_results.csv → figures/S1/data/necrosis_results.csv b/...s/biblio_figure/data/necrosis_results.csv → figures/S1/data/necrosis_results.csv
diff --git a/...biblio_figure/data/pyroptosis_results.csv → figures/S1/data/pyroptosis_results.csv b/...biblio_figure/data/pyroptosis_results.csv → figures/S1/data/pyroptosis_results.csv
diff --git a/...o_figure/figures/cell_death_over_time.png → figures/S1/figures/cell_death_over_time.png b/...o_figure/figures/cell_death_over_time.png → figures/S1/figures/cell_death_over_time.png
diff --git a/...ure/figures/cell_death_over_time_1990.png → .../S1/figures/cell_death_over_time_1990.png b/...ure/figures/cell_death_over_time_1990.png → .../S1/figures/cell_death_over_time_1990.png
diff --git a/...es/biblio_figure/notebooks/biblio_R.ipynb → figures/S1/notebooks/S1.ipynb b/...es/biblio_figure/notebooks/biblio_R.ipynb → figures/S1/notebooks/S1.ipynb
diff --git a/figures/biblio_figure/scripts/biblio_R.r → figures/S1/scripts/biblio_R.r b/figures/biblio_figure/scripts/biblio_R.r → figures/S1/scripts/biblio_R.r
diff --git a/...tal_figure11/figures/PBMCfinal_figure.png → figures/S10/figures/PBMCS10.png b/...tal_figure11/figures/PBMCfinal_figure.png → figures/S10/figures/PBMCS10.png
diff --git a/...MC_redundancy_index_not_shuffled_plot.png → ...MC_redundancy_index_not_shuffled_plot.png b/...MC_redundancy_index_not_shuffled_plot.png → ...MC_redundancy_index_not_shuffled_plot.png
diff --git a/...s/PBMC_redundancy_index_shuffled_plot.png → ...s/PBMC_redundancy_index_shuffled_plot.png b/...s/PBMC_redundancy_index_shuffled_plot.png → ...s/PBMC_redundancy_index_shuffled_plot.png
diff --git a/...supplemental_figure11/notebooks/S11.ipynb → figures/S10/notebooks/S10.ipynb b/...supplemental_figure11/notebooks/S11.ipynb → figures/S10/notebooks/S10.ipynb
@@ -1798,7 +1798,7 @@
     "    \"../\", \n",
     "    \"figures/\",\n",
     "    cell_type,\n",
-    "    \"final_figure.png\")), width = width, height = height, units = \"in\", res = 600\n",
+    "    \"S10.png\")), width = width, height = height, units = \"in\", res = 600\n",
     ")\n",
     "figure\n",
     "dev.off()\n",

diff --git a/...s/S11.supplemental_figure11/scripts/S11.r → figures/S10/scripts/S10.r b/...s/S11.supplemental_figure11/scripts/S11.r → figures/S10/scripts/S10.r
@@ -713,7 +713,7 @@ png(filename = file.path(paste0(
     "../",
     "figures/",
     cell_type,
-    "final_figure.png")), width = width, height = height, units = "in", res = 600
+    "S10.png")), width = width, height = height, units = "in", res = 600
 )
 figure
 dev.off()

diff --git a/...plemental_figure7/figures/Data_splits.png → figures/S11/figures/S11.png b/...plemental_figure7/figures/Data_splits.png → figures/S11/figures/S11.png
diff --git a/..._figure7/figures/data_split_plate_map.png → figures/S11/figures/data_split_plate_map.png b/..._figure7/figures/data_split_plate_map.png → figures/S11/figures/data_split_plate_map.png
diff --git a/...re7/figures/data_split_plate_map_full.png → ...S11/figures/data_split_plate_map_full.png b/...re7/figures/data_split_plate_map_full.png → ...S11/figures/data_split_plate_map_full.png
diff --git a/...7.supplemental_figure7/notebooks/S7.ipynb → figures/S11/notebooks/S11.ipynb b/...7.supplemental_figure7/notebooks/S7.ipynb → 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",

diff --git a/figures/S7.supplemental_figure7/scripts/S7.r → figures/S11/scripts/S11.r b/figures/S7.supplemental_figure7/scripts/S7.r → 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(

diff --git a/...es/S8.supplemental_figure8/figures/S8.png → figures/S12/figures/S12.png b/...es/S8.supplemental_figure8/figures/S8.png → figures/S12/figures/S12.png
diff --git a/...supplemental_figure8/figures/f1_score.png → figures/S12/figures/f1_score.png b/...supplemental_figure8/figures/f1_score.png → figures/S12/figures/f1_score.png
diff --git a/...8.supplemental_figure8/notebooks/S8.ipynb → figures/S12/notebooks/S12.ipynb b/...8.supplemental_figure8/notebooks/S8.ipynb → figures/S12/notebooks/S12.ipynb
@@ -311,15 +311,15 @@
                 "width <- 10\n",
                 "height <- 10\n",
                 "options(repr.plot.width=width, repr.plot.height=height, units = \"cm\", dpi = 600)\n",
-                "fig5 <- (\n",
+                "fig12 <- (\n",
                 "    f1_score_plot\n",
                 "    + theme(plot.tag = element_text(size = 20))\n",
                 ")\n",
-                "fig5\n",
+                "fig12\n",
                 "\n",
                 "# save the plot\n",
                 "\n",
-                "ggsave(\"../figures/S8.png\", fig5, width = width, height = height, dpi = 600)\n"
+                "ggsave(\"../figures/S12.png\", fig12, width = width, height = height, dpi = 600)\n"
             ]
         }
     ],

diff --git a/figures/S8.supplemental_figure8/scripts/S8.r → figures/S12/scripts/S12.r b/figures/S8.supplemental_figure8/scripts/S8.r → figures/S12/scripts/S12.r
@@ -121,13 +121,13 @@ f1_score_plot
 width <- 10
 height <- 10
 options(repr.plot.width=width, repr.plot.height=height, units = "cm", dpi = 600)
-fig5 <- (
+fig12 <- (
     f1_score_plot
     + theme(plot.tag = element_text(size = 20))
 )
-fig5
+fig12
 
 # save the plot
 
-ggsave("../figures/S8.png", fig5, width = width, height = height, dpi = 600)
+ggsave("../figures/S12.png", fig12, width = width, height = height, dpi = 600)
 
diff --git a/figures/S13/figures/S13.png b/figures/S13/figures/S13.png