highlight_profile_plot: Highlight gene and/or taxon of interest on the profile plot

In trvinh/test: PhyloProfile

Description

Highlight gene and/or taxon of interest on the profile plot

Usage

highlight_profile_plot(data, plot_parameter, taxon_highlight, 
    rank_name, gene_highlight)

Arguments

data	data for heatmap plot
plot_parameter	plot parameters (type of x-axis "taxa" or "genes"; names of 2 variables; colors for lowest and highest value of variable 1; colors for lowest and highest value of variable 2; color of co-orthologs; text sizes for x, y axis and legend; legend position "top", "bottom", "right", "left" or "none"; zoom ratio of the co-ortholog dots from -1 to 3; angle of x-axis from 0 to 90; show/hide separate line for reference taxon 1/0; enable/disable coloring gene categories TRUE/FALSE)
taxon_highlight	taxon of interst
rank_name	working taxonomy rank
gene_highlight	gene of interest

Value

A profile heatmap plot with highlighted gene and/or taxon of interest as ggplot object.

Author(s)

Vinh Tran [e-mail]

See Also

data_main_plot, data_customized_plot

Examples

data("full_processed_profile", package="phyloprofile")
plot_df <- data_main_plot(full_processed_profile)
plot_parameter <- list(
    "x_axis" = "taxa",
    "var1_id" = "FAS",
    "var2_id"  = "Traceability",
    "low_color_var1" =  "#FF8C00",
    "high_color_var1" = "#4682B4",
    "low_color_var2" = "#FFFFFF",
    "high_color_var2" = "#F0E68C",
    "para_color" = "#07D000",
    "x_size" = 8,
    "y_size" = 8,
    "legend_size" = 8,
    "main_legend" = "top",
    "dot_zoom" = 0,
    "x_angle" = 60,
    "guideline" = 0,
    "color_by_group" = FALSE
)
taxon_highlight <- "Mammalia"
rank_name <- "class"
gene_highlight <- "OG_1019"
highlight_profile_plot(
    plot_df, plot_parameter, taxon_highlight, rank_name, gene_highlight
)

trvinh/test documentation built on May 9, 2019, 2:26 a.m.