Plotting lineages with ggplot

tidyverse
,
1

Hi all,

I have data for cell lineages that I'd like to plot to get something similar to this:

trackmate-omnipose-tutorial-101
trackmate-omnipose-tutorial-1011073×761 48.3 KB

Using ggraph I was able to make it (almost) work. Here is what I get so far :

suppressMessages({
  library(tidyverse)
  library(ggraph)
  library(igraph)
})
  
edges <- read_csv('test_edges.csv') |>
  filter(Fov == 'C1_5') |>
  graph_from_data_frame(directed = TRUE)

ggraph(edges) +
  geom_edge_link(aes(color = Remove))

image
image663×571 39.9 KB

It looks okayish, but there are two major problems that I can't figure out how to deal with:

  1. The vertical axis in the original plot is a time axis. But I can't figure out how to make it not start from the very top. For example, some of the shorter traces at the right should be somewhere lower based on the time of appearance.
  2. On the x-axis, I'd like to sort tracks based on Track_id, which I also don't understand how to do.

Additionally, when I tried to make facets, it, for some reason, gets wild with the x axis on one of the facets:

edges <- read_csv('test_edges.csv') |>
  graph_from_data_frame(directed = TRUE)

ggraph(edges) +
  geom_edge_link(aes(color = Remove)) +
  facet_edges(facets = vars(Fov), scale = 'free_x')

image
image663×571 72.5 KB

So, the question is whether it is possible to achieve what I want with ggraph? If not, any suggestions on how to make it in R (ggplot2) would be much appreciated.

Sincerely,
Oleg

P.S. For some reason, I'm not allowed to attach csv's, so not sure how to share sample data :confused:

2

A handy way to supply data is to use the dput() function. Do dput(mydata) where "mydata" is the name of your dataset. For really large datasets probably dput(head(mydata, 100). Paste it here between

```

```

1 Like
3

Sample data:

structure(list(Spot_source_id = c(286835, 281727, 291483, 287718, 
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4

Thanks for the data.

I have never used {ggraph} before but I ran your code and

edges <- read_csv('test_edges.csv') |>
  filter(Fov == 'C1_5') |>
  graph_from_data_frame(directed = TRUE)

ggraph(edges) +
  geom_edge_link(aes(color = Remove))

gave me a completely blank plot and

edges <- read_csv('test_edges.csv') |>
  filter(Fov == 'C1_5') |>
  graph_from_data_frame(directed = TRUE)

ggraph(edges) +
  geom_edge_link(aes(color = Remove))

gave me

facets
facets589×520 17.5 KB

I wonder if I have a defective installation ?