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2_panel1.R
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source("R/tests.R", local = T)
source("R/utils.R", local = T)
source("R/constants.R", local = T)
source("R/Cbind.R", local = T)
source("R/plot.R", local = T)
source("R/themes.R", local = T)
source("R/learning_plot.R", local = T)
source("R/summary_plot.R", local = T)
data <- data.table::fread(file = "tidy_data_wide.csv")
genotypes <- c("MB010B.(II)SPARC-Chrimson ISO", "MB010B.(II)SPARC-GFP ISO", "orco 23129")
experiments <- c("20min STM", "20min STM unpaired")
CSs <- c("OCT", "4M1O")
groups <- c("20min STM OCT", "20min STM 4M1O", "20min STM unpaired OCT", "20min STM OCT orco")
valid_reasons <- c("", "?", "Human-override", "Machine-override", "AOJ-override")
panel1_data <- data[
PRE_Reason %in% valid_reasons &
POST_Reason %in% valid_reasons &
Genotype %in% genotypes &
experiment %in% experiments &
CS %in% CSs
]
panel1_data[, Group := paste(experiment, CS)]
panel1_data[, Group := ifelse(grepl(pattern = "orco", x = Genotype), paste(Group, "orco"), Group)]
panel1_data[, experiment := factor(experiment, levels = experiments)]
comparisons <- list(
c("20min STM unpaired OCT", "20min STM OCT"),
c("20min STM unpaired OCT", "20min STM 4M1O"),
c("20min STM unpaired OCT", "20min STM OCT orco")
)
panel1_data <- panel1_data[
Group %in% groups
]
panel1_data[, Group := factor(Group, levels = groups)]
panel1_data[, .N, by=Group]
columns <- c("idoc_folder", "PRE_ROI", "POST_ROI", "Genotype", "experiment", "CS", "PRE", "POST")
export_csvs(panel1_data, "Group", groups, 1, columns)
panel1_data_long <- melt_idoc_data(panel1_data)[, .(Files, Group, id, PI, test, Genotype, CS)]
panel1_data[substr(Files, 1, 10)=="2025-01-06", .(Genotype, PRE_ROI, PRE, POST)]
panel1A <- learning_plot(
panel1_data_long,#[substr(Files, 1, 10)=="2025-01-06",],
"Group",
direction = "horizontal",
y_annotation = 1,
colors = colors_panel1[1:length(groups)],
y_limits = c(-1, 1),
y_breaks = seq(-1, 1, 0.5),
text_vjust = 1.5,
angle_n = 0,
offset = 0.25,
correction = "bonferroni"
)
panel1B <- summary_plot(
panel1_data_long,
group = "Group",
colors = colors_panel1,
comparisons = comparisons,
annotation_y = c(1, 0.9, 1.05)[1:length(comparisons)],
y_limits = c(-1, 1),
y_breaks = seq(-1, 1, 0.5),
geom = "violin+sina",
text_vjust = 1.5,
correction = "bonferroni"
)
panelA <- panel1A$gg + guides(color = "none") +
scale_fill_manual(values = colors_panel1, labels = c("Paired", "Unpaired"))
panelB <- panel1B$gg +
guides(fill = "none", color = "none")
template <- ggplot() + learning_plot_theme
design <- "
AABB
AABB
AABB
AACC
AACC
DDEE
DDEE
DDFF
DDFF
DDFF
"
gg <- template + template +
template + template +
(panelA +
theme(plot.margin = unit(c(0, 0, 40, 0), "pt"))) +
(panelB +
theme(plot.margin = unit(c(30, 0, 0, 0), "pt"))) +
plot_annotation(tag_levels = list(c(LETTERS[1:6]))) +
plot_layout(design=design)
gg
ggsave(plot = gg, filename = paste0(OUTPUT_FOLDER, "/Fig1/Figure_1.pdf"), width = 210, height = 277, unit = "mm")
ggsave(plot = gg, filename = paste0(OUTPUT_FOLDER, "/Fig1/Figure_1.svg"), width = 210, height = 277, unit = "mm")
gg