domain_plotting: Create architecure plot for a single protein
In trvinh/test: PhyloProfile

Description Usage Arguments Value Author(s) See Also Examples

Create architecure plot for a single protein

1 2	domain_plotting(df, geneID, sep, label_size, title_size, min_start, max_end, color_scheme)

`df`	domain dataframe for ploting
`geneID`	ID of seed or orthologous protein
`sep`	separate indicator for title
`label_size`	lable size
`title_size`	title size
`min_start`	the smallest start position of all domains
`max_end`	the highest stop position of all domains
`color_scheme`	color scheme for all domain types

A ggplot object

Vinh Tran tran@bio.uni-frankfurt.de

get_qual_col_for_vector, parse_domain_input

## Not run: 
# get domain data
domain_file <- system.file(
    "extdata", "domain_files/OG_1009.domains",
    package = "phyloprofile", mustWork = TRUE
)
domain_df <- parse_domain_input(seedID, domain_file, "file")
df <- domain_df[domain_df$orthoID == "A.thaliana@3702@241736",]
# create color scheme for all domain types
all_features <- levels(as.factor(df$feature))
all_colors <- get_qual_col_for_vector(all_features)
color_scheme <- structure(
    all_colors,
    .Names = all_features
)
# other parameters
geneID <- "A.thaliana@3702@241736"
sep <- "|"
label_size <- 9
title_size <- 9
min_start <- min(df$start)
max_end <- max(df$end)
# do plotting
domain_plotting(
    df,
    geneID,
    sep,
    label_size, title_size,
    min_start, max_end,
    color_scheme
)

## End(Not run)