How to specify the color of some genes

[uuwuyi]

Hi Wilkox,

I'm now using a palette to colour the genes. But I hope to specify the colour of genes with the name 'na' and keep other genes using the colour from the palette. I can't achieve this by adding a second colour layer. Could you please tell me how can I make this using gggenes? Thank you in advance!

[wilkox]

Hi @ugobananas – I don't quite understand what you're trying to do. Could you post a reprex of what you've done so far and explain what you want it to look like? Thanks!

[uuwuyi]

Hi Wilkox,

Sorry for not posting the codes. I want to keep the genes labeled as 'n' in grey and color other genes using the palette I generated. But I can only get this figure with all the genes colored by the palette.

I tried to extract the 'n' genes into another dataframe, made an additional figure and then tried p1+p2 to merge them together. But it gave the error 'Can't add ggplot(data, aes(xmin = start, xmax = end, y = molecule, fill = gene, to a ggplot object'. Below is my code.

library(ggplot2)
library(gggenes)
library(RColorBrewer)

dummies <- make_alignment_dummies(
  data4,
  aes(xmin=start, xmax=end, y=molecule, id=gene),
  on = "homolog"
)
mycolors <- colorRampPalette(brewer.pal(9, "OrRd"))(46)
p1<-ggplot(data,aes(xmin=start, xmax=end, y=molecule, fill=gene, label=gene, forward=direction))+
  geom_gene_arrow()+facet_wrap(~ molecule, scales="free", ncol=1)+
  theme_genes()+geom_blank(data=dummies, aes(forward=1))+
  scale_fill_manual(values=mycolors)+
  geom_gene_label(align="left")

dummies <- make_alignment_dummies(
  data41,
  aes(xmin=start, xmax=end, y =molecule, id=gene))
p1+ggplot(data41,aes(xmin=start, xmax=end, y=molecule, fill=gene, label=gene, forward=direction))+
  geom_gene_arrow()+facet_wrap(~ molecule, scales="free", ncol=1)+
  theme_genes()+geom_blank(data=dummies, aes(forward=1))+
  scale_color_manual(values=c('n'='grey'))

Could you please give me some suggestions on how to achieve this? Many thanks!

[wilkox]

See below an example of how this can be done using the forcats package.

library(ggplot2)
library(gggenes)
library(RColorBrewer)
library(forcats)

# Prepare a palette of 11 colours + white at the end
mycolours <- c(colorRampPalette(brewer.pal(9, "OrRd"))(11), "#FFFFFF")

# Convert the "gene" variable into a factor with "protD" at the end
example_genes$gene <- fct_relevel(example_genes$gene, "protD", after = Inf)

# Draw the plot with the custom palette
ggplot(example_genes, aes(xmin = start, xmax = end, y = molecule, fill = gene)) +
  geom_gene_arrow() +
  facet_wrap(~ molecule, scales = "free", ncol = 1) +
  scale_fill_manual(values = mycolours) +
  theme_genes()

^{Created on 2020-10-17 by the reprex package (v0.3.0)}