Ggplot2

shadow text effect in grid and ggplot2 graphics

After the release of meme package, I received several feedbacks from users.

The most usefule one is the comment on my blog post:

Sercan Kahveci

Greetings Mr. Yu,

I am very happy that this package exists. Thank you for making it! I would like to request a feature, to ensure the package is able to compete with professional meme-creation tools like memegenerator and paint.net. Since memes often use the font Impact, in white and with black outline, I believe the package would be more powerful if it also did that automatically.

Regards,

Sercan Kahveci, MSc

Content creator at Questionable Research Memes on Facebook https://www.facebook.com/QResearchMemes/

The words, ‘compete with professional meme-creation tools’, stimulated me to develop text plotting with background outline effect.

Now this feature is available in meme v>=0.0.7, which can be downloaded from CRAN.

pixel art of ggplot2 faceting using geofacet

I just discovered an interesting ggplot2 extension, geofacet, that supports arranging facet panels that mimics geographic topoloty.

After playing with it, I realized that it is not only for visualizing geo-related data, but also can be fun for presenting data to mimics pixel art.

Phylomoji with ggtree and emojifont

With ggtree (Yu et al. 2017), it is very easy to create phylomoji. Emoji is internally supported by ggtree.

Use emoji in taxa labels

library(ggtree)
tree_text <- "(((((cow, (whale, dolphin)), (pig2, boar)), camel), fish), seedling);"
x <- read.tree(text=tree_text)
ggtree(x, linetype="dashed", color='firebrick') +
    xlim(NA, 7) + ylim(NA, 8.5) +
    geom_tiplab(aes(color=label), parse='emoji', size=14, vjust=0.25) +
    labs(title="phylomoji", caption="powered by ggtree + emojifont")

add layer to specific panel of facet_plot output

This is a question from ggtree google group:

Dear ggtree team,

how can I apply a geom_xxx to only one facet panel? For example if i want to get geom_hline(yintersect=1:30) or a geom_text() in the dot panel? I cant see the facet_grid(. ~ var) function call, so I don’t know which subsetting to use. I have already read http://stackoverflow.com/questions/29873155/geom-text-and-facets-not-working

  tr <- rtree(30)
  
  d1 <- data.frame(id=tr$tip.label, val=rnorm(30, sd=3))
  p <- ggtree(tr)
  
  p2 <- facet_plot(p, panel="dot", data=d1, geom=geom_point, aes(x=val), color='firebrick')
  d2 <- data.frame(id=tr$tip.label, value = abs(rnorm(30, mean=100, sd=50)))
  
  p3 <- facet_plot(p2, panel='bar', data=d2, geom=geom_segment, aes(x=0, xend=value, y=y, yend=y), size=3, color='steelblue') + theme_tree2()

Thanks! Andreas

If this can be done, we can create even more comprehensive tree plots.

xlim_tree: set x axis limits for only Tree panel

A ggtree user recently asked me the following question in google group:

I try to plot long tip labels in ggtree and usually adjust them using xlim(), however when creating a facet_plot xlim affects all plots and minimizes them.

Is it possible to work around this and only affect the tree and it’s tip labels leaving the other plots in facet_plot unaffected?

This is indeed a desire feature, as ggplot2 can’t automatically adjust xlim for text since the units are in two different spaces (data and pixel).

facet_plot: a general solution to associate data with phylogenetic tree

ggtree provides gheatmap for visualizing heatmap and msaplot for visualizing multiple sequence alignment with phylogenetic tree.

We may have different data types and want to visualize and align them with the tree. For example, dotplot of SNP site (e.g. using geom_point(shape='|')), barplot of trait values (e.g. using geom_barh(stat='identity')) et al.

To make it easy to associate different types of data with phylogenetic tree, I implemented the facet_plot function which accepts a geom function to draw the input data.frame and display it in an additional panel.

reproducible logo generated by ggtree

ggtree provides many helper functions for manupulating phylogenetic trees and make it easy to explore tree structure visually.

Here, as examples, I used ggtree to draw capital character G and C, which are first letter of my name :-).

To draw a tree in such shape, we need fan layout (circular layout with open angle) and then rotating the tree to let the open space on the correct position. Here are the source codes to produce the G and C shapes of tree. I am thinking about using the G shaped tree as ggtree logo. Have fun with ggtree :-)

embed images in ggplot2 via subview and annotate a phylogenetic tree with images using inset function

I extended the subview function to support embed image file in a ggplot object.

set.seed(123)
d = data.frame(x=rnorm(10), y=rnorm(10))

imgfile <- tempfile(, fileext=".png")
download.file("https://avatars1.githubusercontent.com/u/626539?v=3&u=e731426406dd3f45a73d96dd604bc45ae2e7c36f&s=140",
              destfile=imgfile, mode='wb')

p = ggplot(d, aes(x, y))
subview(p, imgfile, x=d$x[1], y=d$y[1]) + geom_point(size=5)

Font Awesome supported in emojifont

CRAN_Status_Badge

emojifont is available in CRAN, you can use the following command to install it.

install.packages("emojifont")

An example of using emoji font in R plot is showed below:

use emoji font in R

I have played with emoji in R for a while. My solution of using it is different from what implemented in emoGG.

emoGG is a good attemp to add emoji in ggplot2. It render emoji picture (png) and creat a layer, geom_emoji, to add emoji.

In my opinion, emoji should be treated as ordinary font in user interface, albeit it maynot be true internally.

It would be more flexible if we can use emoji as ordinary font and in this way user don’t need to learn extra stuff.