help with color_type = "per_symbol" with protein sequences

[ron-geller]

Hi, I would like to generate an EDlogo for a protein sequence (so 20 letters in total) with custom colors. However, I am not finding a way to do it. I manage to get the right colors with the following code: color_profile <- list("type" = "per_symbol", "col" = cols$color) # cols$color has the 20 colors I want in order plogomaker(df[,2:7], color_profile = color_profile) but I cannot figure out how to do this in the logomaker function, which gives me the correct formatting. I tried different things in the logo_control argument with no luck. Can you please let me know how to do this? Thanks, Ron

[kkdey]

Hi Ron,

Can you try this?

library(Logolas) cols1 <- c(rev(RColorBrewer::brewer.pal(12, "Paired"))[c(3,4,7,8,11,12,5,6,9,10)], RColorBrewer::brewer.pal(12, "Set3")[c(1,2,5,8,9)], RColorBrewer::brewer.pal(9, "Set1")[c(9,7)], RColorBrewer::brewer.pal(8, "Dark2")[c(3,4,8)]) names(cols1) = c("A", "C", "D", "E", "F", "G", "H", "I", "K", "L", "M", "N", "P", "Q", "R", "S", "T", "V", "W", "Y")

library(ggseqlogo) data(ggseqlogo_sample) sequence <- seqs_aa$AKT1 logomaker(sequence, type = "EDLogo", colors = cols1)

This should take the colors for the corresponding amino acid monomer character in the cols1 vector. Let me know if it does not work.

[ron-geller]

Hi, Thanks for the answer. However, it is still not giving me the right colors I want... For example: these are my colors cols1 <- c("#f76ab4", "#ff7f00", "#e41a1c", "#e41a1c", "#84380b", "#f76ab4", "#3c58e5", "#12ab0d", "#3c58e5", "#12ab0d", "#12ab0d" ,"#972aa8" ,"#12ab0d", "#972aa8", "#3c58e5", "#ff7f00", "#ff7f00" ,"#12ab0d", "#84380b" ,"#84380b")

names(cols1) = c("A", "C", "D", "E", "F", "G", "H", "I", "K", "L", "M","N", "P", "Q", "R", "S", "T", "V", "W", "Y")

some simulated data

df=data.frame(data=runif(20)) rownames(df)= names(cols1)

the logo plot

logomaker(df,colors=cols1)

The error

If you notice, M is pink and it should be green ("#12ab0d"), as can be see here

barplot(height = df$data,names=names(cols1),col=cols$color)

Thanks in advance Ron

[kkdey]

Hi Ron,

Surprisingly I get the M to be green. Here is the code I ran.

cols1 <- c("#f76ab4", "#ff7f00", "#e41a1c", "#e41a1c", "#84380b", "#f76ab4", "#3c58e5", "#12ab0d", "#3c58e5", "#12ab0d", "#12ab0d" ,"#972aa8" ,"#12ab0d", "#972aa8", "#3c58e5", "#ff7f00", "#ff7f00" ,"#12ab0d", "#84380b" ,"#84380b")

names(cols1) = c("A", "C", "D", "E", "F", "G", "H", "I", "K", "L", "M","N", "P", "Q", "R", "S", "T", "V", "W", "Y") df=data.frame(data=runif(20)) rownames(df)= names(cols1) logomaker(df,colors=cols1)

[kkdey]

Are you using the latest version of the package from Github? In case you are using the Bioc version, can you please switch to the Github version instead?

[ron-geller]

Yes, that was the problem. Updating fixed the color issue. Thanks for making the great tool and helping to resolve the issue so fast.