Create umap figure with ggplot (WayScience#29)

* create umap figure with ggplot

* add DP figure

5_analyze_data/notebooks/UMAP_analysis/umap_figure.r

@@ -0,0 +1,82 @@
+suppressPackageStartupMessages(library(ggplot2))
+suppressPackageStartupMessages(library(dplyr))
+
+# Set paths
+umap_dir <- file.path("..", "..", "data")
+umap_cp_file <- file.path(umap_dir, "norm_fs_embeddings_cp.csv.gz")
+umap_dp_file <- file.path(umap_dir, "norm_fs_embeddings_dp_nuc.csv.gz")
+
+output_fig_dir <- "figures"
+
+umap_cp_fig <- file.path(output_fig_dir, "umap_cp.png")
+umap_dp_fig <- file.path(output_fig_dir, "umap_dp.png")
+
+# Load data
+umap_cp_df <- readr::read_csv(
+    umap_cp_file,
+    col_types = readr::cols(
+        .default = "d",
+        Metadata_Well = "c",
+        Metadata_WellRow = "c",
+        Metadata_gene_name = "c",
+        Metadata_genotype = "c"
+    )
+)
+
+print(dim(umap_cp_df))
+head(umap_cp_df, 3)
+
+umap_cp_gg <- (
+    ggplot(umap_cp_df, aes(x = UMAP1, y = UMAP2))
+    + geom_point(
+        aes(
+            color = Metadata_number_of_singlecells,
+            shape = Metadata_genotype
+        )
+    )
+    + scale_shape_manual(name = "Genotype", values = c(3, 1))
+    + scale_color_gradient(name = "Cell count", low = "green", high = "blue")
+    + theme_bw()
+)
+
+umap_cp_gg
+
+# Output figure
+ggsave(umap_cp_fig, umap_cp_gg, dpi = 500, height = 6, width = 6)
+
+# Load data
+umap_dp_df <- readr::read_csv(
+    umap_dp_file,
+    col_types = readr::cols(
+        .default = "d",
+        Metadata_Well = "c",
+        Metadata_Genotype = "c",
+        Metadata_Genotype_Replicate = "c",
+        Metadata_Model = "c",
+        Metadata_Plate_Map_Name = "c",
+        Metadata_Actin = "c",
+        Metadata_DNA = "c",
+        Metadata_ER = "c"
+    )
+)
+
+print(dim(umap_dp_df))
+head(umap_dp_df, 3)
+
+umap_dp_gg <- (
+    ggplot(umap_dp_df, aes(x = UMAP1, y = UMAP2))
+    + geom_point(
+        aes(
+            color = Metadata_number_of_singlecells,
+            shape = Metadata_Genotype
+        )
+    )
+    + scale_shape_manual(name = "Genotype", values = c(3, 1))
+    + scale_color_gradient(name = "Cell count", low = "green", high = "blue")
+    + theme_bw()
+)
+
+umap_dp_gg
+
+# Output figure
+ggsave(umap_dp_fig, umap_dp_gg, dpi = 500, height = 6, width = 6)