# Enrique Blanco Carmona
# e.blancocarmona@kitz-heidelberg.de
# PhD Student – Clinical Bioinformatics
# Division of Pediatric Neurooncology (B062)
# DKFZ-KiTZ | Germany
scale.grade <- c("Grade 2" = "#1a7d9e",
"Grade 3" = "#9e1a3b",
"Grade 4" = "#576e12")
scale.ident <- c("IDH_ACB_AD_540" = "#E07A5F",
"IDH_ACB_AD_809" = "#F2CC8F",
"IDH_ACB_AD_883" = "#DAA82B",
"IDH_NCH2111" = "#81B29A",
"IDH_NCH536" = "#3E745E",
"IDH_NCH6341" = "#5CADC1",
"IDH_NCH6702" = "#8B6BB8",
"IDH_NCH781" = "#3D405B",
"IDH_ACB_AD_785" = "#ae2012",
"IDH_ACB_AD_832" = "#ca6702",
"IDH_ACB_AD_865" = "#ee9b00",
"IDH_NCH2018" = "#e9d8a6",
"IDH_NCH2157" = "#457b9d",
"IDH_NCH2164" = "#1d3557")
scale.subtype.short <- c("AS" = "#b38b14",
"OD" = "#3c5b8b")
# Load data.
sample.oligo <- readRDS("/omics/odcf/analysis/OE0145_projects/idh_gliomas/Figures_Science/revision/IDH_gliomas_book/datasets/integrated_primary_OD.rds")
sign.scores <- readRDS("/omics/odcf/analysis/OE0145_projects/idh_gliomas/Figures_Science/revision/IDH_gliomas_book/datasets/oligodendroglioma_sign_scores.rds")
corr <- stats::cor(sign.scores)
names(corr) <- stringr::str_replace_all(colnames(corr), "\\.", "-")
# Perform hclust.
clust <- hclust(stats::dist(corr %>% as.data.frame()))
order.use <- colnames(corr)[clust$order]
data.use <- corr %>%
as.data.frame() %>%
tibble::rownames_to_column(var = "Source") %>%
tidyr::pivot_longer(cols = -dplyr::all_of(c("Source")),
names_to = "Target",
values_to = "Corr_score") %>%
dplyr::mutate("Corr_score" = ifelse(.data$Corr_score == 1, NA, .data$Corr_score)) %>%
dplyr::mutate("Patient" = sapply(.data$Source, function(x){stringr::str_split(x, "\\.")[[1]][2]})) %>%
dplyr::mutate("Target" = factor(.data$Target, levels = rev(order.use)),
"Source" = factor(.data$Source, levels = order.use))
data.patient <- data.use %>%
dplyr::select(-dplyr::all_of(c("Corr_score", "Target"))) %>%
dplyr::group_by(.data$Source) %>%
dplyr::summarise("Patient" = unique(.data$Patient)) %>%
dplyr::mutate("Source" = factor(.data$Source, levels = order.use))
data.grade <- data.use %>%
dplyr::left_join(y = {sample.oligo@meta.data %>%
dplyr::select(dplyr::all_of(c("orig.ident", "grade"))) %>%
dplyr::mutate("Patient" = sapply(.data$orig.ident, function(x){stringr::str_split(x, "-")[[1]][2]})) %>%
dplyr::select(-dplyr::all_of("orig.ident")) %>%
tibble::as_tibble()},
by = "Patient",
relationship = "many-to-many") %>%
dplyr::select(-dplyr::all_of(c("Patient", "Corr_score", "Target"))) %>%
dplyr::group_by(.data$Source) %>%
dplyr::summarise("Grade" = unique(.data$grade)) %>%
dplyr::mutate("Source" = factor(.data$Source, levels = order.use))
limits <- c(min(data.use$Corr_score, na.rm = TRUE),
max(data.use$Corr_score, na.rm = TRUE))
scale.setup <- SCpubr:::compute_scales(sample = NULL,
feature = NULL,
assay = NULL,
reduction = NULL,
slot = NULL,
number.breaks = 5,
min.cutoff = NA,
max.cutoff = NA,
flavor = "Seurat",
enforce_symmetry = TRUE,
from_data = TRUE,
limits.use = limits)
p.main <- data.use %>%
ggplot2::ggplot(mapping = ggplot2::aes(x = .data$Source,
y = .data$Target,
fill = .data$Corr_score)) +
ggplot2::geom_tile(color = "white", linewidth = 0, na.rm = TRUE) +
ggplot2::scale_y_discrete(expand = c(0, 0), position = "right") +
ggplot2::scale_x_discrete(expand = c(0, 0),
position = "top") +
ggplot2::coord_equal() +
ggplot2::scale_fill_gradientn(colors = rev(RColorBrewer::brewer.pal(n = 11, name = "RdBu")),
na.value = "grey75",
name = "P. Corr.",
breaks = scale.setup$breaks,
labels = scale.setup$labels,
limits = scale.setup$limits)
p.main <- SCpubr:::modify_continuous_legend(p = p.main,
legend.title = "P. Corr.",
legend.aes = "fill",
legend.type = "colorbar",
legend.position = "bottom",
legend.length = 6,
legend.width = 0.25,
legend.framecolor = "grey50",
legend.tickcolor = "white",
legend.framewidth = 0.2,
legend.tickwidth = 0.2)
p.main <- p.main +
ggplot2::theme_minimal(base_size = 12) +
ggplot2::theme(axis.ticks.x.bottom = ggplot2::element_blank(),
axis.ticks.x.top = ggplot2::element_blank(),
axis.ticks.y.left = ggplot2::element_blank(),
axis.ticks.y.right = ggplot2::element_blank(),
axis.text.y.left = ggplot2::element_blank(),
axis.text.y.right = ggplot2::element_blank(),
axis.text.x.top = ggplot2::element_blank(),
axis.text.x.bottom = ggplot2::element_blank(),
axis.title.x.bottom = ggplot2::element_blank(),
axis.title.x.top = ggplot2::element_blank(),
axis.title.y.right = ggplot2::element_blank(),
axis.title.y.left = ggplot2::element_blank(),
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 = 0.1),
text = ggplot2::element_text(family = "sans"),
plot.caption.position = "plot",
legend.key.size = ggplot2::unit(0.2, 'cm'),
legend.title = ggplot2::element_text(face = "bold", size = 12),
legend.text = ggplot2::element_text(size = 12),
legend.justification = "center",
plot.margin = ggplot2::margin(t = 1, r = 10, b = 0, l = 10),
panel.border = ggplot2::element_rect(fill = NA, color = "black", linewidth = 0.5),
panel.grid.major = ggplot2::element_blank(),
legend.position = "bottom",
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"))
p.orig <- data.patient %>%
dplyr::mutate("Patient_title" = "Patient") %>%
ggplot2::ggplot(mapping = ggplot2::aes(x = .data$Source,
y = .data$Patient_title,
fill = .data$Patient)) +
ggplot2::geom_tile(color = "white", linewidth = 0, na.rm = TRUE) +
ggplot2::scale_y_discrete(expand = c(0, 0), position = "right") +
ggplot2::scale_x_discrete(expand = c(0, 0),
position = "top") +
ggplot2::coord_equal() +
ggplot2::scale_fill_manual(values = scale.ident) +
ggplot2::guides(fill = ggplot2::guide_legend(title.position = "top", title.hjust = 0.5, ncol = 2)) +
ggplot2::theme_minimal(base_size = 12) +
ggplot2::theme(axis.ticks.x.bottom = ggplot2::element_blank(),
axis.ticks.x.top = ggplot2::element_blank(),
axis.ticks.y.left = ggplot2::element_blank(),
axis.ticks.y.right = ggplot2::element_line(color = "black"),
axis.text.y.left = ggplot2::element_blank(),
axis.text.y.right = ggplot2::element_text(face = "bold", color = "black"),
axis.text.x.top = ggplot2::element_blank(),
axis.text.x.bottom = ggplot2::element_blank(),
axis.title.x.bottom = ggplot2::element_blank(),
axis.title.x.top = ggplot2::element_blank(),
axis.title.y.right = ggplot2::element_blank(),
axis.title.y.left = ggplot2::element_blank(),
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 = 0.1),
text = ggplot2::element_text(family = "sans"),
plot.caption.position = "plot",
legend.justification = "center",
legend.key.size = ggplot2::unit(0.2, 'cm'),
legend.title = ggplot2::element_text(face = "bold", size = 12),
legend.text = ggplot2::element_text(size = 12),
plot.margin = ggplot2::margin(t = 0, r = 10, b = 0.75, l = 10),
panel.border = ggplot2::element_rect(fill = NA, color = "black", linewidth = 0.5),
panel.grid.major = ggplot2::element_blank(),
legend.position = "bottom",
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"))
p.grade <- data.grade %>%
dplyr::mutate("Grade_title" = "Grade") %>%
ggplot2::ggplot(mapping = ggplot2::aes(x = .data$Source,
y = .data$Grade_title,
fill = .data$Grade)) +
ggplot2::geom_tile(color = "white", linewidth = 0, na.rm = TRUE) +
ggplot2::scale_y_discrete(expand = c(0, 0), position = "right") +
ggplot2::scale_x_discrete(expand = c(0, 0),
position = "top") +
ggplot2::coord_equal() +
ggplot2::scale_fill_manual(values = scale.grade) +
ggplot2::guides(fill = ggplot2::guide_legend(title.position = "top", title.hjust = 0.5, ncol = 1)) +
ggplot2::theme_minimal(base_size = 12) +
ggplot2::theme(axis.ticks.x.bottom = ggplot2::element_blank(),
axis.ticks.x.top = ggplot2::element_blank(),
axis.ticks.y.left = ggplot2::element_blank(),
axis.ticks.y.right = ggplot2::element_line(color = "black"),
axis.text.y.left = ggplot2::element_blank(),
axis.text.y.right = ggplot2::element_text(face = "bold", color = "black"),
axis.text.x.top = ggplot2::element_blank(),
axis.text.x.bottom = ggplot2::element_blank(),
axis.title.x.bottom = ggplot2::element_blank(),
axis.title.x.top = ggplot2::element_blank(),
axis.title.y.right = ggplot2::element_blank(),
axis.title.y.left = ggplot2::element_blank(),
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 = 0.1),
text = ggplot2::element_text(family = "sans"),
plot.caption.position = "plot",
legend.justification = "center",
legend.key.size = ggplot2::unit(0.2, 'cm'),
legend.title = ggplot2::element_text(face = "bold", size = 12),
legend.text = ggplot2::element_text(size = 12),
plot.margin = ggplot2::margin(t = 0, r = 10, b = 0.75, l = 10),
panel.border = ggplot2::element_rect(fill = NA, color = "black", linewidth = 0.5),
panel.grid.major = ggplot2::element_blank(),
legend.position = "bottom",
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"))
design <- "A
B
C"
p <- patchwork::wrap_plots(A = p.grade,
B = p.orig,
C = p.main,
design = design, guides = "collect") +
patchwork::plot_annotation(theme = ggplot2::theme(legend.position = "bottom"))
