make_pic {ontophylo}

Assign colors to picture ID layers

Description

Assigns colors to picture ID layers (@paths) of an object of class 'Picture'. The object should be a PS or ESP vector illustration imported using the grImport package. Colors are taken from cols.maps argument were the palette indicates the scale of the desired statistics for the evolutionary rates.

Usage

make_pic(picture, layers, cols.maps)

Arguments

picture

grImport object. A vector image imported in R using the 'readPicture' function from grImport.

layers

numeric. A named vector where values indicate the layer IDs in the Picture object and names indicate the anatomy ontology term labels.

cols.maps

character. A named vector where elements correspond to color IDs and names indicate the anatomy ontology term labels.

Value

An object of class 'Picture' with the assigned colors to different anatomical regions.

Author(s)

Sergei Tarasov

Examples

data("HAO", "hym_graph", "hym_img", "hym_kde")
# Get picture.
picture <- hym_img
# Get picture layers from three anatomical regions.
terms_list <- as.list(c("HAO:0000397", "HAO:0000576", "HAO:0000626"))
terms_list <- setNames(terms_list, c("head", "mesosoma", "metasoma"))
anat_layers <- get_vector_ids_list(terms = terms_list , ONT = HAO, GR = hym_graph)
# Get mean rates all branches for the three anatomical regions.
plot_stat <- lapply(hym_kde, function(x) unlist(lapply(x$loess.lambda.mean, function(x) mean(x) )) )
plot_stat <- do.call(cbind, plot_stat)
# Add two columns for the other anatomical regions (just for this example).
plot_stat <- cbind(plot_stat, plot_stat*0.75, plot_stat*0.5)
colnames(plot_stat) <- c("head", "mesosoma", "metasoma")
# Select an arbitrary branch.
plot_stat <- plot_stat[5,]
# Set scale.
scale_lim <- range(plot_stat)
# Get color palette.
hm.palette <- colorRampPalette(RColorBrewer::brewer.pal(9, "Spectral"), space = "Lab")
cols_maps <- make_colors_relative_scale(plot_stat, palette = hm.palette(100),
                                        lims = scale_lim)
# Plot picture.
new_pic <- make_pic(picture, anat_layers, cols_maps)
grImport::grid.picture(new_pic)