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custom_plot_function.R
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#### 主题 ----
theme_cat <- function(...) {
theme(
axis.title = element_text(
size = 8,
face = "plain",
colour = "black"
),
axis.text = element_text(
size = 8,
face = "plain",
colour = "black"
),
axis.line = element_blank(),
axis.ticks = element_line(
size = 0.25,
lineend = "square",
colour = "black"
),
panel.background = element_blank(),
panel.grid = element_blank(),
panel.border = element_rect(
size = 0.25,
fill = NA,
colour = "black"
),
legend.background = element_blank(),
legend.title = element_text(
size = 8,
face = "plain",
colour = "black"
),
legend.text = element_text(
size = 8,
face = "plain",
colour = "black"
),
legend.key = element_blank(),
legend.key.height = unit(8, "pt"),
legend.key.width = unit(8, "pt"),
plot.background = element_blank(),
plot.title = element_text(
size = 8,
hjust = 0.5,
face = "plain",
colour = "black"
),
plot.margin = margin(
t = 0,
r = 0,
b = 0,
l = 0
),
strip.background = element_blank(),
strip.text = element_text(
size = 8,
face = "plain",
colour = "black"
),
...
)
}
cc <- c(
"#1e7fa0",
"#e94929",
"#62be9d",
"#004ea2",
"#f4abac",
"#bee0d0",
"#a91e32",
"#eab946",
"#c36625",
"#f0c800",
"#a8cd34",
"#c3e0e7",
"#672e1d",
"#874154",
"#e0c4ce",
"#ad5942",
"#a58262",
"#d5b210",
"#141722",
"#434c50",
"#f0f0f4"
)
catbarplot <- function(adata,
x,
y,
fill = NULL,
position = "stack",
width = 0.8,
title = NULL,
xlab = NULL,
ylab = NULL,
legend = TRUE,
errorbar = FALSE,
sort = FALSE,
flip = FALSE,
group_by = NULL,
label_position = NULL,
hline = NULL,
jitter = FALSE) {
x <- enquo(x)
y <- enquo(y)
fill <- enquo(fill)
group_by <- enquo(group_by)
if (sort) {
adata <- adata %>%
mutate({{ x }} := fct_reorder({{ x }}, {{ y }}))
}
if (as_label(group_by) != "NULL") {
adata <- adata %>%
mutate({{ x }} := fct_reorder({{ x }}, {{ group_by }}))
}
if (as_label(fill) %in% colnames(adata) & !errorbar) {
p <- adata %>%
ggplot(aes(x = {{ x }}, y = {{ y }}, fill = {{ fill }})) +
geom_bar(
stat = "identity",
width = width,
position = position
)
}
if (!(as_label(fill) %in% colnames(adata)) & !errorbar) {
fill <- as_label(fill) %>% str_replace_all("\"", "")
if (fill == "NULL") {
fill <- cc[1]
}
p <- adata %>%
ggplot(aes(x = {{ x }}, y = {{ y }})) +
geom_bar(
stat = "identity",
width = width,
position = position,
fill = fill
)
}
if (errorbar) {
if (as_label({{ x }}) == as_label({{ fill }})) {
adata <- adata %>% group_by({{ x }})
}
if (as_label({{ x }}) != as_label({{ fill }})) {
adata <- adata %>% group_by({{ x }}, {{ fill }})
}
p <- adata %>%
summarise(mean = mean({{ y }}), sd = sd({{ y }})) %>%
ggplot(aes(x = {{ x }}, y = mean, fill = {{ fill }})) +
geom_errorbar(
mapping = aes(
x = {{ x }},
ymin = mean - sd,
ymax = mean + sd
),
width = 0.2,
size = 0.5 * 0.36,
color = "black",
position = position_dodge(width)
) +
geom_bar(
stat = "identity",
width = width,
position = position
)
}
if (flip) {
p <- p + coord_flip() +
labs(y = xlab, x = ylab, title = title)
}
if (!flip) {
p <- p +
labs(x = xlab, y = ylab, title = title)
}
p <- p +
theme_cat() +
scale_fill_manual(values = cc)
if (!legend) {
p <- p + guides(fill = "none")
}
if (!is.null(hline)) {
p <- p + geom_hline(
yintercept = hline,
color = "white",
linetype = "dashed",
size = 0.5
)
}
if (!is.null(label_position)) {
match.arg(label_position, c("inward", "outward"))
if (label_position == "inward") {
adata <- adata %>%
mutate(hjust = if_else({{ y }} > 0, "inward", "outward")) %>%
mutate(temp_label = if_else({{ y }} > 0, str_c(" ", {{ x }}), str_c({{ x }}, " ")))
}
if (label_position == "outward") {
adata <- adata %>%
mutate(hjust = if_else({{ y }} > 0, "outward", "inward")) %>%
mutate(temp_label = if_else({{ y }} > 0, str_c({{ x }}, " "), str_c(" ", {{ x }})))
}
p <- p + geom_text(
data = adata,
aes(
x = {{ x }},
y = 0,
label = temp_label,
hjust = hjust
),
size = 6 * 0.36
) +
theme(
axis.text.y = element_blank(),
axis.ticks.y = element_blank()
)
}
return(p)
}
#### 气泡图 ----
catlabel <- function(adata, flip = F) {
adata <-
p <- adata %>%
rename_at(1, ~"x") %>%
arrange_at(2) %>%
mutate(x = as_factor(x)) %>%
ggplot() +
geom_tile(aes_string(
x = "x",
y = 1,
fill = colnames(adata)[2]
)) +
theme_void() +
theme(
strip.text = element_text(size = 6, colour = "black"),
legend.title = element_text(size = 6, colour = "black"),
legend.text = element_text(size = 6, colour = "black"),
legend.key.height = unit(6, "pt"),
legend.key.width = unit(6, "pt")
)
if (flip) {
p <- p + coord_flip()
}
return(p)
}
catdotplot <- function(adata,
x,
y,
color,
size,
title = NULL,
annotation_row = NULL,
annotation_col = NULL,
cluster_row = FALSE,
cluster_col = FALSE,
dot_scale = 6) {
x <- enquo(x)
y <- enquo(y)
size <- enquo(size)
color <- enquo(color)
if (!is.null(annotation_col)) {
x_order <- annotation_col %>% pull(1)
adata <- adata %>%
mutate(x = as_factor(x)) %>%
mutate(x = fct_relevel(x, x_order))
}
if (!is.null(annotation_row)) {
y_order <- annotation_row %>% pull(1)
adata <- adata %>%
mutate(y = as_factor(y)) %>%
mutate(y = fct_relevel(y, y_order))
}
p <- adata %>%
ggplot(aes(
x = {{ x }},
y = {{ y }},
size = {{ size }},
color = {{ color }}
)) +
geom_point() +
theme_cat() +
theme(
axis.text.x = element_text(
angle = 90,
hjust = 1,
vjust = 0.5,
colour = "black",
size = 6,
),
axis.text.y = element_text(
colour = "black",
size = 6
),
axis.title = element_blank(),
legend.title = element_text(size = 6),
legend.text = element_text(size = 6),
legend.key.size = unit(6, "pt"),
legend.key = element_blank(),
legend.margin = margin(r = 0, unit = "pt"),
plot.title = element_text(
size = 6,
colour = "black",
face = "plain",
hjust = 0.5
)
) +
scale_color_gradient2(low = "#00a6e1", mid = "white", high = "#ee6470") +
scale_radius(range = c(0, dot_scale))
if (!is.null(title)) {
p <- p + labs(title = title)
}
if (!is.null(annotation_col)) {
pc <- catlabel(annotation_col) +
scale_fill_manual(values = paletteer::paletteer_d("RColorBrewer::Set3"))
p <- p %>%
aplot::insert_top(pc, height = 0.02)
}
if (!is.null(annotation_row)) {
pr <- catlabel(annotation_row, flip = T)
p <- p %>%
aplot::insert_right(pr, width = 0.02)
}
if (cluster_row) {
cluster_row <- adata %>%
ungroup() %>%
select(x, y, {{ color }}) %>%
pivot_wider(names_from = x, values_from = {{ color }}) %>%
replace(is.na(.), 0) %>%
column_to_rownames("y") %>%
dist() %>%
hclust() %>%
ggtree::ggtree()
p <- p %>%
aplot::insert_left(cluster_row, width = 0)
}
if (cluster_col) {
cluster_col <- adata %>%
ungroup() %>%
select(x, y, {{ color }}) %>%
pivot_wider(names_from = y, values_from = {{ color }}) %>%
replace(is.na(.), 0) %>%
column_to_rownames("x") %>%
dist() %>%
hclust() %>%
ggtree::ggtree() +
ggtree::layout_dendrogram()
p <- p %>%
aplot::insert_top(cluster_col, height = 0)
}
return(p)
}
catscatter <-
function(adata,
x,
y,
color = NULL,
size = NULL,
method = NULL,
cutoff_x = NULL,
cutoff_y = NULL) {
sub_adata <-
adata %>% dplyr::select({{ x }}, {{ y }}, {{ color }}, {{ size }})
if (!is.null(cutoff_x)) {
sub_adata <- sub_adata %>%
filter({{ x }} > cutoff_x)
}
if (!is.null(cutoff_y)) {
sub_adata <- sub_adata %>%
filter({{ y }} > cutoff_y)
}
p <- sub_adata %>%
ggplot2::ggplot(ggplot2::aes(
x = {{ x }},
y = {{ y }},
color = {{ color }},
size = {{ size }}
)) +
geom_point_rast(
size = 0.5,
color = "grey",
fill = "black", raster.dpi = 600
) +
ggrastr::rasterise(ggplot2::geom_point(
size = 0.5,
color = "grey",
fill = "black"
),
dpi = 600) +
theme_cat()
if (!is.null(method)) {
cor_res <-
pull(sub_adata, {{ x }}) %>% cor.test(pull(sub_adata, {{ y }}), method = method)
p_value <- cor_res$p.value
estimate <- cor_res$estimate
p <- p +
ggplot2::geom_smooth(
method = "lm",
formula = y ~ x,
color = "#6b76ae",
fill = "#e5a323",
size = 0.5,
alpha = 0.2
) +
ggplot2::labs(title = paste0(
"r = ",
round(estimate, 2),
", p = ",
format(p_value, digits = 2, scientific = T)
))
}
return(p)
}
#### 棒棒糖图 ----
catlollipop <- function() {
}
#### 散点图 ----
catpoint <- function(adata,
x,
y,
fill,
color,
label = NULL,
text = NULL,
title = NULL,
xlab = NULL,
ylab = NULL,
legend = TRUE) {
adata <- adata %>%
dplyr::rename(
x = {{ x }},
y = {{ y }},
color = {{ color }},
label = {{ label }}
)
if (!is.null(text)) {
adata <-
adata %>% mutate(label = ifelse(label %in% text, label, ""))
}
p <- adata %>%
ggplot(aes(x = x, y = y, color = color)) +
geom_point() +
labs(x = xlab, y = ylab, title = title) +
theme_cat(aspect.ratio = 1)
if (!is.null(label)) {
p <- p + ggrepel::geom_text_repel(
aes(label = label),
max.overlaps = 1000000,
color = "black",
size = 3.5
)
}
if (!legend) {
p <- p + guides(color = "none")
}
return(p)
}
#### 火山图 ----
library(tidyverse)
catvolcano <-
function(adata,
x,
y,
label,
text = NULL,
p_value = 0.05,
log2FC = 0.25) {
adata <- adata %>%
dplyr::rename(x = {{ x }}, y = {{ y }}, label = {{ label }})
adata <- adata %>%
mutate(change = ifelse(
y <= p_value & abs(x) >= log2FC,
ifelse(x >= log2FC, "Upregulated", "Downregulated"),
"Stable"
))
max_x <- ceiling(max(abs(adata$x)))
if (!is.null(text)) {
adata <- adata %>% mutate(label = ifelse(label %in% text, text, ""))
}
print(adata %>% count(change))
p <- adata %>%
ggplot(aes(
x = x,
y = -log10(y),
colour = change
)) +
ggrastr::geom_point_rast(raster.dpi = 600, size = 0.5) +
geom_vline(
xintercept = c(-log2FC, log2FC),
lty = 2,
col = "black",
lwd = 0.5
) +
geom_hline(
yintercept = -log10(p_value),
lty = 2,
col = "black",
lwd = 0.5
) +
labs(
x = "log2(Fold change)",
y = "-log10 (P value)"
) +
scale_color_manual(
values = c("#00a6e1", "lightgrey", "#ee6470"),
labels = c(
str_c(
"Down (",
adata %>% count(change) %>% filter(change == "Downregulated") %>% pull(n),
")"
),
"Stable",
str_c(
"Up (",
adata %>% count(change) %>% filter(change == "Upregulated") %>% pull(n),
")"
)
)
) +
theme_cat() +
theme(
aspect.ratio = 1,
legend.position = "top",
legend.title = element_blank(),
legend.margin = margin(b = -8)
) +
xlim(c(-max_x, max_x))
# theme(
# plot.title = element_blank(),
# legend.position = "top",
# legend.title = element_blank(),
# legend.text = element_text(size = 6, colour = "black"),
# legend.key = element_blank(),
# aspect.ratio = 1,
# panel.background = element_blank(),
# panel.grid = element_blank(),
# axis.text = element_text(size = 6, colour = "black"),
# axis.ticks = element_line(size = 0.5, colour = "black"),
# axis.line = element_blank(),
# axis.title = element_text(size = 6, colour = "black"),
# panel.border = element_rect(
# size = 0.5,
# colour = "black",
# fill = F
# )
# )
if (!is.null(text)) {
p <- p + ggrepel::geom_text_repel(
aes(label = label),
max.overlaps = 1000,
color = "black",
size = 3.5,
fontface = "italic"
)
}
return(p)
}
#### GSEA ----
tableGrob2 <- function(d, p = NULL) {
d <- d[order(rownames(d)), ]
tp <- gridExtra::tableGrob(d,
theme = gridExtra::ttheme_minimal(base_size = 6)
)
if (is.null(p)) {
return(tp)
}
p_data <- ggplot_build(p)$data[[1]]
p_data <- p_data[order(p_data[["group"]]), ]
pcol <- unique(p_data[["colour"]])
j <- which(tp$layout$name == "rowhead-fg")
for (i in seq_along(pcol)) {
tp$grobs[j][[i + 1]][["gp"]] <- grid::gpar(col = pcol[i])
}
return(tp)
}
catgsea <-
function(x,
geneSetID,
title = "",
color = "#8ac45f",
base_size = 6,
rel_heights = c(1.6, 0.4, 1),
subplots = 1:3,
pvalue_table = FALSE,
ES_geom = "line") {
ES_geom <- match.arg(ES_geom, c("line", "dot"))
geneList <- position <- NULL
if (length(geneSetID) == 1) {
gsdata <- enrichplot:::gsInfo(x, geneSetID)
} else {
gsdata <-
do.call(rbind, lapply(geneSetID, enrichplot:::gsInfo, object = x))
}
p <- ggplot(gsdata, aes_(x = ~x)) +
xlab(NULL) +
theme_cat() +
theme(axis.line.x.bottom = element_blank()) +
scale_x_continuous(expand = c(0, 0))
if (ES_geom == "line") {
es_layer <- geom_line(aes_(y = ~runningScore, color = ~Description),
size = 0.5
)
} else {
es_layer <-
geom_point(
aes_(y = ~runningScore, color = ~Description),
size = 0.5,
data = subset(gsdata, position == 1)
)
}
p.res <- p + es_layer + theme(
legend.position = c(0.8, 0.8),
legend.title = element_blank(),
legend.background = element_rect(fill = "transparent")
)
p.res <- p.res + ylab("Enrichment Score") + theme(
axis.text.x = element_blank(),
axis.ticks.x = element_blank(),
axis.line.x = element_blank(),
plot.margin = margin(
t = 0,
r = 0,
b = 0,
l = 0,
unit = "cm"
)
)
i <- 0
for (term in unique(gsdata$Description)) {
idx <- which(gsdata$ymin != 0 & gsdata$Description ==
term)
gsdata[idx, "ymin"] <- i
gsdata[idx, "ymax"] <- i + 1
i <- i + 1
}
p2 <- ggplot(gsdata, aes_(x = ~x)) +
geom_linerange(aes_(
ymin = ~ymin,
ymax = ~ymax,
color = ~Description
)) +
theme_classic(base_size) +
theme(
legend.position = "none",
plot.margin = margin(t = 0, b = 0),
axis.ticks = element_blank(),
axis.text = element_blank(),
axis.line.x = element_blank(),
axis.line.x.bottom = element_blank(),
axis.line.y.left = element_blank(),
panel.border = element_rect(
size = 0.25,
fill = NA,
colour = "black"
),
plot.title = element_blank(),
axis.title = element_blank()
) +
scale_x_continuous(expand = c(
0,
0
)) +
scale_y_continuous(expand = c(0, 0))
if (length(geneSetID) == 1) {
v <- seq(1, sum(gsdata$position), length.out = 9)
inv <- findInterval(rev(cumsum(gsdata$position)), v)
if (min(inv) == 0) {
inv <- inv + 1
}
col <-
c(
rev(RColorBrewer::brewer.pal(5, "Blues")),
RColorBrewer::brewer.pal(
5,
"Reds"
)
)
ymin <- min(p2$data$ymin)
yy <- max(p2$data$ymax - p2$data$ymin) * 0.3
xmin <- which(!duplicated(inv))
xmax <-
xmin + as.numeric(table(inv)[as.character(unique(inv))])
d <- data.frame(
ymin = ymin,
ymax = yy,
xmin = xmin,
xmax = xmax,
col = col[unique(inv)]
)
p2 <- p2 + geom_rect(
aes_(
xmin = ~xmin,
xmax = ~xmax,
ymin = ~ymin,
ymax = ~ymax,
fill = ~ I(col)
),
data = d,
alpha = 0.9,
inherit.aes = FALSE
)
}
df2 <- p$data
df2$y <- p$data$geneList[df2$x]
p.pos <- p + geom_segment(
data = df2,
aes_(
x = ~x,
xend = ~x,
y = ~y,
yend = 0
),
color = "grey"
)
p.pos <-
p.pos + ylab("Ranked List Metric") + xlab("Rank in Ordered Dataset") +
theme(plot.margin = margin(
t = -0.1,
r = 0.2,
b = 0.2,
l = 0.2,
unit = "cm"
))
if (!is.null(title) && !is.na(title) && title != "") {
p.res <- p.res + ggtitle(title)
}
if (length(color) == length(geneSetID)) {
p.res <- p.res + scale_color_manual(values = color)
if (length(color) == 1) {
p.res <- p.res + theme(legend.position = "none")
p2 <- p2 + scale_color_manual(values = "black")
} else {
p2 <- p2 + scale_color_manual(values = color)
}
}
if (pvalue_table) {
pd <- x[geneSetID, c("Description", "NES", "qvalues")]
colnames(pd)[3] <- c("FDR")
pd <- pd[, -1]
pd <- round(pd, 2)
if (length(geneSetID) == 1) {
rownames(pd) <- ""
# pd <- as.data.frame(t(pd))
# pd$V2 <- c("NES", "FDR")
# pd <- pd[,c("V2", "V1")]
}
print(pd)
tp <- tableGrob2(pd, p.res)
p.res <-
p.res + theme(legend.position = "none") + annotation_custom(
tp,
xmin = quantile(p.res$data$x, 0.75),
xmax = quantile(
p.res$data$x,
0.8
),
ymin = quantile(
p.res$data$runningScore,
0.6
),
ymax = quantile(
p.res$data$runningScore,
0.8
)
)
}
plotlist <- list(p.res, p2, p.pos)[subplots]
n <- length(plotlist)
plotlist[[n]] <- plotlist[[n]] + theme(
axis.line.x = element_line(),
axis.ticks.x = element_line(),
axis.text.x = element_text()
)
if (length(subplots) == 1) {
# return(plotlist[[1]] + theme(plot.margin = margin(
# t = 0.2,
# r = 0.2, b = 0.2, l = 0.2, unit = "cm"
# )))
return(plotlist[[1]])
}
if (length(rel_heights) > length(subplots)) {
rel_heights <- rel_heights[subplots]
}
aplot::plot_list(
gglist = plotlist,
ncol = 1,
heights = rel_heights
)
}
#### 小提琴图 ----
catviolin <- function(adata,
x,
y,
fill = NULL,
title = NULL,
xlab = NULL,
ylab = NULL,
legend = TRUE,
sort = FALSE,
flip = FALSE,
hline = NULL,
group_by = NULL) {
x <- enquo(x)
y <- enquo(y)
fill <- enquo(fill)
group_by <- enquo(group_by)
if (sort) {
adata <- adata %>%
mutate({{ x }} := fct_reorder({{ x }}, {{ y }}))
}
if (as_label(group_by) != "NULL") {
adata <- adata %>%
mutate({{ x }} := fct_reorder({{ x }}, {{ group_by }}))
}
p <- adata %>%
ggplot(aes(x = {{ x }}, y = {{ y }}, fill = {{ fill }})) +
geom_violin()
if (flip) {
p <- p + coord_flip() +
labs(y = xlab, x = ylab, title = title)
}
if (!flip) {
p <- p +
labs(x = xlab, y = ylab, title = title)
}
p <- p +
theme_cat() +
scale_fill_manual(values = cc)
if (!legend) {
p <- p + guides(fill = "none")
}
if (!is.null(hline)) {
p <- p + geom_hline(
yintercept = hline,
color = "white",
linetype = "dashed",
size = 0.5
)
}
return(p)
}
#### scWGCNA网咯 ----
catModuleNetworkPlot <-
function(seurat_obj,
mods = "all",
outdir = "ModuleNetworks",
plot_size = c(6, 6),
wgcna_name = NULL,
label_center = FALSE,
edge.alpha = 0.25,
vertex.label.cex = 1,
vertex.size = 6,
n_hubs = 25,
n_center = 10,
text = "",
n_conns = 500,
...) {
if (is.null(wgcna_name)) {
wgcna_name <- seurat_obj@misc$active_wgcna
}
MEs <- GetMEs(seurat_obj, wgcna_name)
modules <- GetModules(seurat_obj, wgcna_name)
if (mods == "all") {
mods <- levels(modules$module)
mods <- mods[mods != "grey"]
}
if (!dir.exists(outdir)) {
dir.create(outdir)
}
cat(paste0("Writing output files to ", outdir))
TOM <- GetTOM(seurat_obj, wgcna_name)
n_hubs <- n_hubs
hub_list <- lapply(mods, function(cur_mod) {
cur <- subset(modules, module == cur_mod)
cur <- cur[, c("gene_name", paste0("kME_", cur_mod))] %>%
top_n(n_hubs)
colnames(cur)[2] <- "var"
cur %>%
arrange(desc(var)) %>%
.$gene_name
})
names(hub_list) <- mods
for (cur_mod in mods) {
print(cur_mod)
cur_color <- modules %>%
subset(module == cur_mod) %>%
.$color %>%
unique()
n_genes <- n_hubs
n_conns <- n_conns
cur_kME <- paste0("kME_", cur_mod)
cur_genes <- hub_list[[cur_mod]]
matchind <- match(cur_genes, colnames(TOM))
reducedTOM <- TOM[matchind, matchind]
orderind <- order(reducedTOM, decreasing = TRUE)
connections2keep <- orderind[1:n_conns]
reducedTOM <- matrix(0, nrow(reducedTOM), ncol(reducedTOM))
reducedTOM[connections2keep] <- 1
if (label_center) {
cur_genes[(n_center + 1):n_hubs] <- ""
}
gA <-
graph.adjacency(
as.matrix(reducedTOM[1:n_center, 1:n_center]),
mode = "undirected",
weighted = TRUE,
diag = FALSE
)
gB <-
graph.adjacency(
as.matrix(reducedTOM[
(n_center + 1):n_genes,
(n_center + 1):n_genes
]),
mode = "undirected",
weighted = TRUE,
diag = FALSE
)
layoutCircle <- rbind(layout.circle(gA) / 2, layout.circle(gB))
g1 <-
graph.adjacency(
as.matrix(reducedTOM),
mode = "undirected",
weighted = TRUE,
diag = FALSE
)
pdf(
paste0(outdir, "/", cur_mod, ".pdf"),
width = plot_size[1],
height = plot_size[2],
useDingbats = FALSE
)
print(cur_genes)
print(class(cur_genes))
cur_genes[!(cur_genes %in% text)] <- ""
print(cur_genes)
print(class(g1))
plot(
g1,
edge.color = adjustcolor(cur_color, alpha.f = 0.25),
edge.alpha = edge.alpha,
vertex.color = cur_color,
vertex.label = as.character(cur_genes),
vertex.label.dist = 1.1,
vertex.label.degree = -pi / 4,
vertex.label.color = "black",
vertex.label.family = "Helvetica",
vertex.label.font = 3,
vertex.label.cex = vertex.label.cex,
vertex.frame.color = "black",
layout = jitter(layoutCircle),
vertex.size = vertex.size,
main = paste(cur_mod)
)
dev.off()
}
}
#### compass ----
plot_differential_scores <- function(adata, title, text) {
adata <- adata %>%
mutate(show_text = if_else(reaction_name %in% text, reaction_name, "")) %>%
mutate(change = if_else(
abs(cohens_d) > 0 &
adjusted_pval <= 0.1,
if_else(cohens_d > 0, "Up", "Down"),
"Stable"
))
max_x <- ceiling(max(abs(adata$cohens_d)))
adata %>% ggplot(aes(
x = cohens_d,
y = -log10(adjusted_pval),
color = change
)) +
geom_point() +
labs(x = "Cohen's d", y = "-log10 (Wilcoxon-adjusted p)", title = title) +
geom_hline(yintercept = -log10(0.1), linetype = "dashed") +
geom_vline(xintercept = 0, linetype = "dashed") +
theme_cat() +
theme(
aspect.ratio = 1,
legend.position = "bottom",
legend.title = element_blank(),
legend.margin = margin(t = -10)