Description Usage Arguments Examples
Allows the user to plot a multiple alignent using ggplot's grammar of graphics
1 2 3 4 5 6 7 | drawAlignment(infile, seqlist, alignment_labels, wrap = FALSE,
wrap_length = NULL, roi = FALSE, roi_data = NULL,
consensus = FALSE, consensus_height = 5, funct_assoc = FALSE,
funct_assoc_data = NULL, funct_assoc_height = 5,
highlights = FALSE, highlights_data = NULL, hlines = FALSE,
hlines_data = NULL, tick_spacing = 5, ticks_text_size = 30,
order = NULL, color_pal = NULL)
|
infile |
The alignment to use (fasta file) |
seqlist |
A dataframe with metadata for the alignment |
alignment_labels |
The name of the column to label the entries in the alignment with |
wrap |
TRUE/FALSE whether to use a column of plots to show the alignment |
wrap_length |
Length at which to cut the wrap |
roi |
TRUE/FALSE whether to only show regions of interest in the alignment |
roi_data |
Dataframe defining the regions to show |
consensus |
TRUE/FALSE whether to include a consensus line in the alignment |
consensus_height |
Height of the consensus line plot |
funct_assoc |
TRUE/FALSE whether to show functional associations in the alignment |
funct_assoc_data |
Columns in the metadata dataframe to use in searching for functional association (e.g. "c(sterol~other, sterol~cyclo)") |
funct_assoc_height |
Height of the functional association lines |
highlights |
TRUE/FALSE whether to highlight certain sites in the alignment |
highlights_data |
Dataframe specifying which site to highlight |
hlines |
TRUE/FALSE whether to divide the alignment with horizontal lines |
hlines_data |
Dataframe specifying where to divide alignment |
tick_spacing |
Spacing between x-axis ticks |
ticks_text_size |
Size of x-axis ticks text |
order |
Order in which to display the members of the alignment |
color_pal |
Color palette to use |
1 |
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