Generate Supplemental Figure 2

4.figures/nbconverted/SuppFigure2_Plate4_platemaps.r

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+suppressPackageStartupMessages(library(dplyr))
+suppressPackageStartupMessages(library(ggplot2))
+suppressPackageStartupMessages(library(grid))
+suppressPackageStartupMessages(library(patchwork))
+suppressPackageStartupMessages(library(platetools))
+
+figure_dir <- "figures/supplementary"
+output_supp_figure_2 <- file.path(figure_dir, "supp_figure_2_plate4_platemaps.png")
+
+url <- "https://raw.githubusercontent.com/WayScience/nf1_cellpainting_data/main/0.download_data/metadata/platemap_NF1_plate4.csv"
+plate_4_df <- read.csv(url)
+
+dim(plate_4_df)
+head(plate_4_df)
+
+platemap_dose <- platetools::raw_map(
+    data = as.character(plate_4_df$Concentration),
+    well = plate_4_df$well_position,
+    plate = 96,
+    size = 8
+) +
+ggtitle(paste("siRNA treatment and dose platemap")) +
+theme(plot.title = element_text(size = 12, face = "bold")) +
+ggplot2::geom_point(aes(shape = plate_4_df$siRNA)) +
+ggplot2::scale_shape_discrete(
+    name = "siRNA Treatments",
+    limits = c("None", "Scramble", "NF1 Target 1", "NF1 Target 2"),
+    guide = guide_legend(override.aes = list(size = 3))  # Adjust size here
+) +
+ggplot2::scale_fill_manual(
+    name = "Concentrations (nM)",
+    values = c("#ffffff", "#d9f0d9", "#a3e8a3", "#6ed46e", "#3ab93a", "#007a00")
+) +
+theme(
+    legend.text = element_text(size = 10),
+    legend.title = element_text(size = 12),
+    legend.position = "right",
+    # move legend around so it fits better on the screen
+    legend.margin = margin(-15, 0, 10, 0),
+    legend.box = "vertical",
+    axis.text.x = element_text(size = 10),  # Adjust x-axis tick size
+    axis.text.y = element_text(size = 10)   # Adjust y-axis tick size
+)
+
+platemap_dose
+
+
+# Platemap for genotype
+platemap_genotype <- platetools::raw_map(
+    data = plate_4_df$genotype,
+    well = plate_4_df$well_position,
+    plate = 96,
+    size = 8
+) +
+ggtitle(paste("Genotype platemap")) +
+theme(plot.title = element_text(size = 12, face = "bold")) +
+ggplot2::scale_fill_discrete(name = "Genotype") +
+theme(
+    legend.text = element_text(size = 10),
+    legend.title = element_text(size = 12),
+    legend.position = "right",
+    # move legend around so it fits better on the screen
+    legend.margin = margin(-10, 0, 10, 0),
+    legend.box = "horizontal",
+    axis.text.x = element_text(size = 10),  # Adjust x-axis tick size
+    axis.text.y = element_text(size = 10)   # Adjust y-axis tick size
+)
+
+platemap_genotype
+
+
+align_plot_gg <- (
+    platemap_dose /
+    platemap_genotype
+) + plot_layout(heights = c(1, 1))
+
+supp_fig_2_gg <- (
+  align_plot_gg
+) + plot_annotation(tag_levels = "A") & theme(plot.tag = element_text(size = 15))
+
+# Save or display the plot
+ggsave(output_supp_figure_2, dpi = 500, height = 8, width = 8)
+
+supp_fig_2_gg

figure_environment.yml

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+name: nf1_figures
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - conda-forge::jupyter
+  - conda-forge::jupyterlab
+  - conda-forge::ipykernel
+  - conda-forge::python
+  - conda-forge::r-irkernel
+  - conda-forge::nb_conda_kernels
+  - conda-forge::widgetsnbextension
+  - conda-forge::jupyter_contrib_nbextensions
+  - conda-forge::r-base=4.2.2
+  - conda-forge::r-dplyr=1.0.10
+  - conda-forge::r-tidyr
+  - conda-forge::r-readr
+  - conda-forge::r-stringr
+  - conda-forge::r-ggplot2
+  - conda-forge::r-ggrepel
+  - conda-forge::r-gridextra
+  - conda-forge::r-devtools
+  - conda-forge::r-reshape2
+  - conda-forge::r-cowplot
+  - conda-forge::r-patchwork
+  - conda-forge::r-magick
+  - conda-forge::r-platetools
+  - conda-forge::r-arrow
+  - bioconda::bioconductor-complexheatmap