order of the genome names

[ramadatta]

Hi,

Thanks for wonderful package.

I am trying to align according to a specific gene using make_alignment_dummies but the order of the genomes in the final figure are sorted by genome names. This results me a figure, where a few genomes on top are similar and a few genomes with the same gene contents due to different names are sorted by names are seen at the bottom.

Is there a way to sort the genomes based on the gene content? or else is there a way ggplot can plot the data exactly in the same order passed by dummies and example_genes if have sorted the contents?

Thanks much!

[wilkox]

Hi ramadatta, you can set the order of the genomes (or indeed any categorical variable mapped to an axis) by making that variable a factor.

If this doesn't work or you need some more help, could you post the code you already have as a reprex?

[ramadatta]

Thanks much @wilkox . Will come back to you soon on this.

[ramadatta]

library(ggplot2)
library(gggenes)

dummies <- make_alignment_dummies(
  example_genes,
  aes(xmin = start, xmax = end, y = molecule, id = gene),
  on = "genE"
)

ggplot(example_genes, aes(xmin = start, xmax = end, y = factor(molecule), fill = gene)) +
  geom_gene_arrow() +
  geom_blank(data = dummies) +
  facet_wrap(~ molecule, scales = "free", ncol = 1) +
  scale_fill_brewer(palette = "Set3") +
  theme_genes()

# Creating a presence/absence matrix for example genes

PA_matrix <- as.data.frame(with(example_genes, table(molecule, gene)) > 0L) +0L
PA_matrix
#>         genA genB genC genD genE genF protA protB protC protD protE protF
#> Genome1    1    1    1    1    1    1     0     0     1     1     1     1
#> Genome2    1    1    1    1    1    1     1     1     0     0     0     0
#> Genome3    1    1    1    1    1    1     1     1     0     0     0     0
#> Genome4    1    1    1    1    1    1     0     0     0     0     0     0
#> Genome5    1    1    1    1    1    1     0     0     1     1     1     1
#> Genome6    1    1    1    1    1    1     1     1     0     0     0     0
#> Genome7    0    1    1    1    1    1     1     1     1     1     1     1
#> Genome8    0    1    1    1    1    1     1     1     1     1     1     1

# Sorting the presence/absence matrix for example genes

sorted_PA_matrix <- PA_matrix[do.call(order,as.data.frame(PA_matrix)),]
sorted_PA_matrix
#>         genA genB genC genD genE genF protA protB protC protD protE protF
#> Genome7    0    1    1    1    1    1     1     1     1     1     1     1
#> Genome8    0    1    1    1    1    1     1     1     1     1     1     1
#> Genome4    1    1    1    1    1    1     0     0     0     0     0     0
#> Genome1    1    1    1    1    1    1     0     0     1     1     1     1
#> Genome5    1    1    1    1    1    1     0     0     1     1     1     1
#> Genome2    1    1    1    1    1    1     1     1     0     0     0     0
#> Genome3    1    1    1    1    1    1     1     1     0     0     0     0
#> Genome6    1    1    1    1    1    1     1     1     0     0     0     0

sorted_genomes <- row.names(sorted_PA_matrix)
sorted_genomes
#> [1] "Genome7" "Genome8" "Genome4" "Genome1" "Genome5" "Genome2" "Genome3"
#> [8] "Genome6"

# Creating sorted_dummies and sorted_example_genes which the final output figure should reflect
sorted_dummies <- dummies[order(unlist(sapply(dummies$molecule, function(x) which(sorted_genomes == x)))),]
sorted_example_genes <- example_genes[order(unlist(sapply(example_genes$molecule, function(x) which(sorted_genomes == x)))),]

#head(example_genes)
#head(sorted_example_genes)

ggplot(sorted_example_genes, aes(xmin = start, xmax = end, y = factor(molecule), fill = gene)) +
  geom_gene_arrow() +
  geom_blank(data = sorted_dummies) +
  facet_wrap(~ molecule, scales = "free", ncol = 1) +
  scale_fill_brewer(palette = "Set3") +
  theme_genes()

Hi @wilkox ,

Thank you very much for passing the reprex link. It was useful.

Accordingly, I need the final output figure above in the order of the genomes found in the "sorted_PA_matrix". Passing sorted_examples_genes and sorted_dummies and using factor(molecule), could not help me generate the correct order of genomes intended. Can request to know if I am missing something here? Many thanks in advance.

[wilkox]

library(ggplot2)
library(gggenes)

dummies <- make_alignment_dummies(
  example_genes,
  aes(xmin = start, xmax = end, y = molecule, id = gene),
  on = "genE"
)

# Creating a presence/absence matrix for example genes
PA_matrix <- as.data.frame(with(example_genes, table(molecule, gene)) > 0L) +0L

# Sorting the presence/absence matrix for example genes
sorted_PA_matrix <- PA_matrix[do.call(order,as.data.frame(PA_matrix)),]

sorted_genomes <- row.names(sorted_PA_matrix)

# Creating sorted_dummies and sorted_example_genes which the final output figure should reflect
sorted_dummies <- dummies[order(unlist(sapply(dummies$molecule, function(x) which(sorted_genomes == x)))),]
sorted_example_genes <- example_genes[order(unlist(sapply(example_genes$molecule, function(x) which(sorted_genomes == x)))),]

# Convert molecule variable to a factor
sorted_example_genes$molecule <- factor(sorted_example_genes$molecule, levels = unique(sorted_example_genes$molecule))
sorted_dummies$molecule <- factor(sorted_dummies$molecule, levels = unique(sorted_dummies$molecule))

ggplot(sorted_example_genes, aes(xmin = start, xmax = end, y = factor(molecule), fill = gene)) +
  geom_gene_arrow() +
  geom_blank(data = sorted_dummies) +
  facet_wrap(~ molecule, scales = "free", ncol = 1) +
  scale_fill_brewer(palette = "Set3") +
  theme_genes()

^{Created on 2020-07-08 by the reprex package (v0.3.0.9001)}

[ramadatta]

Thank you so much for this @wilkox. This is what I needed.