Pfthb

I made this Volcano plot and am hoping to improve it as follows:

1. fully shade the region with blue data points: with my current code, I wasn't able to extend the shade beyond what you see. I would like it to go all the way to the plot area limits.




2. geom_text allowed me to label a subset of data points, but doing it with ggrepel should add lines connecting the data points with labels thus improving labeling clarity. How can I reuse the existing geom_text code in ggrepel to achieve this?

Here is my code:

ggplot(vol.new, aes(x = log2.fold.change, y = X.NAME., fill = Color)) + # Define data frame to be used for plotting; define data for x and y axes; crate a scatterplot object.

 geom_point(size = 2, shape = 21, colour = "black") + # Define data point style.

 ggtitle(main.title, subtitle = "Just a little subtitle") + # Define title and subtitle.

 labs(x = x.lab, y = y.lab) + # Define labels for x and y axes.

 scale_x_continuous(limits = c(-3, 3), breaks = seq(-3, 3, by = 0.5)) + # Define x limits, add ticks.
 scale_y_continuous(limits = c(0, 6), breaks = seq(0, 6, by = 1)) + # Define y limits, add ticks.

 theme(
 plot.title = element_text(family = "Arial", size = 11, hjust = 0), # Title size and font.
 plot.subtitle = element_text(family = "Arial", size = 11), # Subtitle size and font.
 axis.text = element_text(family = "Arial", size = 10), # Size and font of x and y values.
 axis.title = element_text(family = "Arial", size = 10), # Size and font of x and y axes.
 panel.border = element_rect(colour = "black", fill = NA, size = 1), # Black border around the plot area.
 axis.ticks = element_line(colour = "black", size = 1), # Style of x and y ticks.
 legend.position = "none"
 ) + # Remove legend.

 geom_hline(yintercept = 1.30103, colour = "black", linetype = "dashed", size = 0.75) + # Horizontal significance cut-off line.
 geom_vline(xintercept = 0.584963, colour = "black", linetype = "dashed", size = 0.75) + # Vertical significance cut-off line (+).
 # geom_vline (xintercept = -0.584963, colour = "black", linetype = "dashed", size = 0.75) #Vertical significance cut-off line (-)

 scale_fill_manual(breaks = c("blue", "red"), values = c("deepskyblue3", "firebrick1")) + # Costum colors of data points based on "PursFur" column.

 geom_text(aes(label = ifelse(PursFur == 1, as.character(Protein.ID), "")), hjust = 0, vjust = -0.25) + # Add identifiers to a subset of data points.

 annotate("text", x = 2.9, y = 1.45, label = "P = 0.05", size = 4, fontface = "bold") + # Label to horizontal cut-off line.
 annotate("text", x = 0.68, y = 5.9, label = "1.5-fold", size = 4, fontface = "bold", srt = 90) + # Label to vertical cut-off line.
 annotate("rect", xmin = 0.584963, xmax = 3, ymin = 1.30103, ymax = 6, alpha = .2) # Shade plot subregion.

As suggested in the comments by @hrbrmstr and @zx8754, here are the modifications I made to the code above.

To solve the shading problem (via @hrbrmstr):

annotate ("rect", xmin = 0.584963, xmax = Inf, ymin = 1.30103, ymax = Inf, alpha = .2)

To solve the labeling question (via @zx8754):

geom_label_repel (aes (label = ifelse (PursFur == 1, as.character (Protein.ID), '')), nudge_x = 1.3, direction = "x")

And here is the outcome after these two changes:

See this website and this nice ggrepel tutorial to dive further into the second part of my initial question.

An alternative labeling solution was achieved with the following code:

 geom_label_repel (aes (label = ifelse (PursFur == 1, as.character (Protein.ID),'')), 
 nudge_x = 4, direction = "y",
 arrow = arrow (length = unit (0.02, "npc"), type = "closed", ends = "last", angle = 15),
 fill = "white")

And the resulting plot looks like this now: