Creating dot plots for alignment visualization can be executed using the following steps:

1. Load the libraries and sequences:

library(Biostrings)
library(ggplot2)
library(dotplot)
seqs <- readAAStringSet(file.path(getwd(), "datasets", "ch4", "bhlh.fa"))

2. Make a basic dot plot:

dotPlotg(as.character(seqs[[1]]), as.character(seqs[[2]] ))

3. Change the dot plot and apply the ggplot2 themes and labels:

dotPlotg(as.character(seqs[[1]]), as.character(seqs[[2]] ), wsize=7, wstep=5, nmatch=4) + 
theme_bw() + 
labs(x=names(seqs)[1], y=names(seqs)[2] )

4. Make a function that will create a dot plot from sequences provided and the sequence index:

make_dot_plot <- function(i=1, j=1, seqs = NULL){
 seqi <- as.character(seqs[[i]])
 seqj <- as.character(seqs[[j]])
 namei <- names(seqs)[i]
 namej <- names(seqs)[j]
 return( dotPlotg(seqi, seqj ) + theme_bw() + labs(x=namei, y=namej) )
}

5. Set up data structures to run the function:

combinations <- expand.grid(1:length(seqs),1:length(seqs))
plots <- vector("list", nrow(combinations) )

6. Run the function on all the possible combinations of pairs of sequences:

for (r in 1:nrow(combinations)){
 i <- combinations[r,]$Var1[[1]]
 j <- combinations[r,]$Var2[[1]]
 plots[[r]] <- make_dot_plot(i,j, seqs)
}

7. Plot the grid of plots:

cowplot::plot_grid(plotlist = plots)