Is it possible to avoid axis label overlapping by ggrepel? - r

Question

I am drawing heatmap with ggplot2. Several ticks on y axis need to be labeled. However,some of them are too close and overlap. I know ggrepel could separate text labels, but currently I have not worked out for my problem.
My code is as following. Any suggestion is welcome. Thanks.
Code:
df <- data.frame()
for (i in 1:50){
tmp_df <- data.frame(cell=paste0("cell", i),
gene=paste0("gene", 1:100), exp = rnorm(100), ident = i %% 5)
df<-rbind(df, tmp_df)
}
labelRow=rep("", 100)
for (i in c(2, 5, 7, 11, 19, 23)){
labelRow[i] <- paste0("gene", i)
}
library(ggplot2)
heatmap <- ggplot(data = df, mapping = aes(x = cell, y = gene, fill = exp)) +
geom_tile() +
scale_fill_gradient2(name = "Expression") +
scale_y_discrete(position = "right", labels = labelRow) +
facet_grid(facets = ~ident,
drop = TRUE,
space = "free",
scales = "free", switch = "x") +
scale_x_discrete(expand = c(0, 0), drop = TRUE) +
theme(axis.line = element_blank(),
axis.ticks = element_blank(),
axis.title.y = element_blank(),
axis.text.y = element_text(),
axis.title.x = element_blank(),
axis.text.x = element_blank(),
strip.text.x = element_text(angle = -90))
heatmap

Answer 1

For these kinds of problems, I prefer to draw the axis as a separate plot and then combine. It takes a bit of fiddling but allows you to draw pretty much any axis you want.
In my solution, I'm using the functions get_legend(), align_plots(), and plot_grid() from the cowplot package. Disclaimer: I'm the package author.
library(ggplot2)
library(cowplot); theme_set(theme_gray()) # undo cowplot theme setting
library(ggrepel)
df<-data.frame()
for (i in 1:50){
tmp_df <- data.frame(cell=paste0("cell", i),
gene=paste0("gene", 1:100), exp=rnorm(100), ident=i%%5)
df<-rbind(df, tmp_df)
}
labelRow <- rep("", 100)
genes <- c(2, 5, 7, 11, 19, 23)
labelRow[genes] <- paste0("gene ", genes)
# make the heatmap plot
heatmap <- ggplot(data = df, mapping = aes(x = cell,y = gene, fill = exp)) +
geom_tile() +
scale_fill_gradient2(name = "Expression") +
scale_x_discrete(expand = c(0, 0), drop = TRUE) +
facet_grid(facets = ~ident,
drop = TRUE,
space = "free",
scales = "free", switch = "x") +
theme(axis.line = element_blank(),
axis.title = element_blank(),
axis.text = element_blank(),
axis.ticks = element_blank(),
strip.text.x = element_text(angle = -90),
legend.justification = "left",
plot.margin = margin(5.5, 0, 5.5, 5.5, "pt"))
# make the axis plot
axis <- ggplot(data.frame(y = 1:100,
gene = labelRow),
aes(x = 0, y = y, label = gene)) +
geom_text_repel(min.segment.length = grid::unit(0, "pt"),
color = "grey30", ## ggplot2 theme_grey() axis text
size = 0.8*11/.pt ## ggplot2 theme_grey() axis text
) +
scale_x_continuous(limits = c(0, 1), expand = c(0, 0),
breaks = NULL, labels = NULL, name = NULL) +
scale_y_continuous(limits = c(0.5, 100.5), expand = c(0, 0),
breaks = NULL, labels = NULL, name = NULL) +
theme(panel.background = element_blank(),
plot.margin = margin(0, 0, 0, 0, "pt"))
# align and combine
aligned <- align_plots(heatmap + theme(legend.position = "none"), axis, align = "h", axis = "tb")
aligned <- append(aligned, list(get_legend(heatmap)))
plot_grid(plotlist = aligned, nrow = 1, rel_widths = c(5, .5, .7))