data <- sample@meta.data %>%
dplyr::select(dplyr::all_of(c("final_annotation", "subtype", "orig.ident"))) %>%
tibble::as_tibble() %>%
dplyr::filter(!.data$orig.ident %in% c("IDH_NCH2164", "IDH_NCH6702")) %>%
dplyr::mutate("subtype" = ifelse(.data$subtype == "Oligodendroglioma", "OD", "AS")) %>%
dplyr::mutate("subtype" = factor(.data$subtype, levels = c("OD", "AS"))) %>%
dplyr::group_by(.data$subtype, .data$orig.ident, .data$final_annotation) %>%
dplyr::summarise("n" = dplyr::n(),
"subtype" := unique(.data$subtype),
"final_annotation" := unique(.data$final_annotation)) %>%
dplyr::reframe("freq" = .data$n / sum(.data$n),
"subtype" := unique(.data$subtype),
"final_annotation" := unique(.data$final_annotation),
"orig.ident" := unique(.data$orig.ident))
p <- data %>%
ggpubr::ggboxplot(x = "subtype",
y = "freq",
color = "black",
fill = "subtype",
facet.by = "final_annotation",
short.panel.labs = TRUE,
width = 0.9,
outlier.color = "black",
outlier.alpha = 0,
fatten = 1,
key_glyph = "rect",
nrow = 1,
outlier.shape = NA) +
ggplot2::geom_point(color = "black", size = 2) +
ggplot2::scale_fill_manual(values = scale.subtype.short,
name = "") +
ggpubr::stat_compare_means(mapping = ggplot2::aes(label = "p = ", ggplot2::after_stat(p.format)),
method = "wilcox.test",
comparisons = list(c("OD", "AS")),
paired = FALSE,
position = "jitter") +
ggplot2::theme_minimal(base_size = 20) +
ggplot2::labs(x = "Subtype", y = "Proportion") +
ggplot2::theme(axis.ticks.x.bottom = ggplot2::element_line(color = "black"),
axis.ticks.x.top = ggplot2::element_blank(),
axis.ticks.y.left = ggplot2::element_line(color = "black"),
axis.ticks.y.right = ggplot2::element_blank(),
axis.text.y.left = ggplot2::element_text(color = "black", face = "plain"),
axis.text.y.right = ggplot2::element_blank(),
axis.text.x.top = ggplot2::element_blank(),
axis.text.x.bottom = ggplot2::element_text(color = "black", face = "plain"),
strip.text.x.top = ggplot2::element_text(color = "black", face = "plain"),
axis.title.x.bottom = ggplot2::element_text(color = "black", face = "bold"),
axis.title.x.top = ggplot2::element_blank(),
axis.title.y.right = ggplot2::element_blank(),
axis.title.y.left = ggplot2::element_text(color = "black", face = "bold"),
strip.text = ggplot2::element_text(face = "bold", color = "black"),
axis.line = ggplot2::element_blank(),
plot.title = ggplot2::element_text(face = "bold", hjust = 0),
plot.subtitle = ggplot2::element_text(hjust = 0),
plot.caption = ggplot2::element_text(hjust = 1),
plot.title.position = "plot",
panel.grid = ggplot2::element_blank(),
panel.grid.minor.y = ggplot2::element_line(color = "white", linewidth = 1),
text = ggplot2::element_text(family = "sans"),
plot.caption.position = "plot",
legend.text = ggplot2::element_text(face = "bold"),
legend.title = ggplot2::element_text(face = "bold"),
legend.justification = "center",
plot.margin = ggplot2::margin(t = 40, r = 10, b = 0, l = 10),
panel.border = ggplot2::element_rect(fill = NA, color = "black", linewidth = 1),
panel.grid.major = ggplot2::element_blank(),
legend.position = "none",
legend.spacing = ggplot2::unit(10, unit = "mm"),
plot.background = ggplot2::element_rect(fill = "white", color = "white"),
panel.background = ggplot2::element_rect(fill = "white", color = "white"),
legend.background = ggplot2::element_rect(fill = "white", color = "white"),
legend.key = ggplot2::element_rect(linewidth = 1, color = "white"),
legend.key.size = ggplot2::unit(1, 'lines'))
