Theme used for ggplot figures_28016764
Created by James Santangelo, last modified on Jul 04, 2018
When plotting figures with ggplot, the code for any given figure can often be unwieldy due to the large number of aesthetic adjustments we impose to make the figures look pretty. However, we take advantage of the fact that ggplot objects are built layer-by-layer. Because, we often want many of our figure to look similar, this means we can save our favourite theme as an object and simply add it to out base ggplot objects to produce a figure with the desired appearance.
Below is a figure from a recent paper produced using the default ggplot aesthetics. The figure itself isn't important but the point is that it doesn't look spectacular. For example, the grid is distracting, the points are small, the labels are small and on the x-axis are almost overlapping and the axes do not stand out. I used the following code to produce this figure.
MeanSlope_Sel_Mig <- ggplot(MeansProps_Gen250, aes(x = max_s, y = mean, group = factor(Mig_rate))) +
geom_errorbar(aes(ymin = mean - ci_mean, ymax = mean + ci_mean), width=0.15, size=0.7,
position = position_dodge(width = 0.35)) +
geom_line(size = 1, aes(linetype = factor(Mig_rate)), position = position_dodge(width = 0.35)) +
geom_point(size = 3.5, aes(fill = factor(Mig_rate), shape = factor(Mig_rate)), position = position_dodge(width = 0.35)) +
scale_shape_manual(labels = c("0", "0.01", "0.05"), values = c(21, 22, 23)) +
scale_fill_manual(labels = c("0", "0.01", "0.05"), values = c("white", "grey60", "black")) +
scale_linetype_manual(labels = c("0", "0.01", "0.05"), values = c("dotted", "dashed", "solid")) +
ylab("Mean slope") + xlab("Selection coefficient") +
coord_cartesian(ylim = c(-0.007, 0.038)) + scale_y_continuous(breaks = seq(from = -0.006, to = 0.036, by = 0.006)) +
labs(fill = "Migration rate", shape = "Migration rate", linetype = "Migration rate")
To make this figure publication quality, we can create a 'theme' object, which can also be used to produce other figures in the project. The theme object may look something like this (I have been using this theme for every figure for the last 9 years and only slightly modify it as needed).
ggplot_theme <- theme(aspect.ratio=0.9,panel.background = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.border=element_blank(),
axis.line.x = element_line(color="black",size=1),
axis.line.y = element_line(color="black",size=1),
axis.ticks=element_line(color="black"),
axis.text=element_text(color="black",size=15),
axis.title=element_text(color="black",size=1),
axis.title.y=element_text(vjust=2,face="bold",size=15),
axis.title.x=element_text(vjust=0.1,face="bold",size=15),
axis.text.x=element_text(size=15,angle=45,hjust=1),
axis.text.y=element_text(size=15),
legend.position = "right", legend.direction="vertical",
legend.text=element_text(size=11), legend.key = element_rect(fill = "white"),
legend.title = element_text(size=13,face="bold"),legend.key.size = unit(0.5, "cm"))
All we have to do now is add this theme to our plot object, as follow:
MeanSlope_Sel_Mig + ggplot_theme
Doing so produces the following figure:
[Figure_ex_noTheme.pdf](attachments/28016764/28016762.pdf)
(application/pdf)
Document generated by Confluence on May 22, 2024 11:44