Add supp fig 2 (#69)

* add supp fig 2

* update supp fig 1 folder name

3.figures/supp_figure_1_splitbyplate/SuppFigure1_splitbyplate.ipynb → 3.figures/supp_figure_1/SuppFigure1_splitbyplate.ipynb

@@ -44,8 +44,7 @@
     "suppressPackageStartupMessages(library(dplyr))\n",
     "suppressPackageStartupMessages(library(ggplot2))\n",
     "suppressPackageStartupMessages(library(grid))\n",
-    "suppressPackageStartupMessages(library(patchwork))\n",
-    "suppressPackageStartupMessages(library(platetools))"
+    "suppressPackageStartupMessages(library(patchwork))"
    ]
   },
   {

3.figures/supp_figure_2/scripts/SuppFigure2_qualitycontrol.r

@@ -0,0 +1,117 @@
+suppressPackageStartupMessages(library(dplyr))
+suppressPackageStartupMessages(library(ggplot2))
+suppressPackageStartupMessages(library(grid))
+suppressPackageStartupMessages(library(patchwork))
+suppressPackageStartupMessages(library(arrow))
+
+figure_dir <- "../figures/supplementary"
+output_supp_figure_2 <- file.path(figure_dir, "supp_figure_2_qualitycontrol.png")
+
+# Path to UMAP results
+qc_results_dir <- file.path(
+    "../../../nf1_cellpainting_data/1.cellprofiler_ic/image_quality_control"
+)
+
+# Load data
+qc_results_file <- file.path(qc_results_dir, "concat_img_quality_data.parquet")
+
+qc_results_df <- arrow::read_parquet(qc_results_file)
+
+# Remove any plate 4 image sets
+qc_results_df <- qc_results_df %>% dplyr::filter(Metadata_Plate != "Plate_4")
+
+dim(qc_results_df)
+head(qc_results_df)
+
+width <- 18
+height <- 6
+options(repr.plot.width = width, repr.plot.height = height)
+
+# Ensure the Channel factor has the correct order
+qc_results_df$Channel <- factor(qc_results_df$Channel, levels = c("DAPI", "GFP", "CY5", "RFP"))
+
+# Threshold values
+upper_threshold <- -1.36839084751248
+lower_threshold <- -2.4936740062477365
+
+# Create the plot with the specified color mapping
+qc_blur_plot <- ggplot(qc_results_df, aes(x = ImageQuality_PowerLogLogSlope, fill = Channel)) +
+    geom_density(alpha = 0.5, adjust = 1.5) + 
+    scale_fill_manual(
+        values = c("DAPI" = "#4472C4",  # Blue
+                   "GFP" = "#70AD47",  # Green
+                   "CY5" = "#D35B9D",  # Brighter magenta
+                   "RFP" = "#b42718")  # Red
+    ) +
+    geom_vline(aes(xintercept = upper_threshold, color = paste("Upper =", round(upper_threshold, 2))), 
+               linetype = "dashed", linewidth = 1.2) + 
+    geom_vline(aes(xintercept = lower_threshold, color = paste("Lower =", round(lower_threshold, 2))), 
+               linetype = "dashed", linewidth = 1.2) +  
+    scale_color_manual(name = "QC Thresholds", values = c("Upper = -1.37" = "red", 
+                                                          "Lower = -2.49" = "red")) +  # Set the color and label for the legend
+    labs(
+        x = "PowerLogLogSlope",
+        y = "Density"
+    ) +
+    theme_bw() +
+    facet_wrap(~ Metadata_Plate) +  # Facet by plate
+    theme(
+        strip.text = element_text(size = 16),   # Facet titles
+        axis.title = element_text(size = 16),  # Axis titles
+        axis.text = element_text(size = 14),   # Axis text
+        legend.title = element_text(size = 16), # Legend title
+        legend.text = element_text(size = 14)   # Legend text
+    )
+
+qc_blur_plot
+
+
+width <- 15
+height <- 8
+options(repr.plot.width = width, repr.plot.height = height)
+
+# Take natural logarithm plus one of the percent maximal for better visualization
+qc_results_df <- qc_results_df %>%
+  mutate(LogImageQuality = log1p(ImageQuality_PercentMaximal))
+
+# Create a label for the threshold line
+original_threshold <- 1.4
+
+# Create the plot
+qc_saturation_plot <- ggplot(qc_results_df, aes(x = LogImageQuality)) +
+  geom_histogram(binwidth = 0.1, fill = "lightblue", color = "black") +
+  facet_wrap(~ Metadata_Plate) +
+  geom_vline(aes(xintercept = log1p(original_threshold), 
+                 color = paste("Threshold =", original_threshold, "%")),
+             linetype = "dashed", size = 1) +
+  scale_color_manual(name = "QC Threshold", values = "red") + # Customize the legend title and color
+  labs(
+    x = "Natural Logarithm of (Image Quality Percentage + 1)",
+    y = "Count"
+  ) +
+  theme_bw() +
+  theme(
+    strip.text = element_text(size = 16),   # Facet titles
+    axis.title = element_text(size = 16),  # Axis titles
+    axis.text = element_text(size = 14),   # Axis text
+    legend.title = element_text(size = 16), # Legend title
+    legend.text = element_text(size = 14)   # Legend text
+  )
+
+qc_saturation_plot
+
+align_plot <- (
+    qc_blur_plot /
+    qc_saturation_plot 
+) + plot_layout(heights= c(2,2))
+
+align_plot
+
+supp_fig_2_gg <- (
+  align_plot
+) + plot_annotation(tag_levels = "A") & theme(plot.tag = element_text(size = 25))
+
+# Save or display the plot
+ggsave(output_supp_figure_2, plot = supp_fig_2_gg, dpi = 500, height = 8, width = 12)
+
+supp_fig_2_gg