highlightProfilePlotCr: Highlight gene and/or taxon of interest on the phylogenetic...

In trvinh/PhyloProfileRibi: PhyloProfileRibi

Description

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

Usage

highlightProfilePlotCr(data, plotParameter = NULL, taxonHighlight =
    "none", rankName = "none", geneHighlight = "none")

Arguments

data	dataframe for plotting the heatmap phylogentic profile (either full or subset profiles)
plotParameter	plot parameters, including (1) type of x-axis "taxa" or "genes" - default = "taxa"; (2+3) names of 2 variables var1ID and var2ID - default = "var1" & "var2"; (4) color for lowest var1 - default = "#FF8C00"; (5) color for highest var1 - default = "#4682B4"; (6) color for lowest var2 - default = "#FFFFFF", (7) color for highest var2 - default = "#F0E68C", (8) color of co-orthologs - default = "#07D000"; (9+10+11) text sizes for x, y axis and legend - default = 9 for each; (12) legend position "top", "bottom", "right", "left" or "none" - default = "top"; (13) zoom ratio of the co-ortholog dots from -1 to 3 - default = 0; (14) angle of x-axis from 0 to 90 - default = 60; (14) show/hide separate line for reference taxon 1/0 - default = 0; (15) enable/disable coloring gene categories TRUE/FALSE - default = FALSE). NOTE: Leave blank or NULL to use default values.
taxonHighlight	taxon of interst. Default = "none".
rankName	working taxonomy rank (needed only for highlight taxon).
geneHighlight	gene of interest. Default = "none".

Value

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

Author(s)

Vinh Tran [e-mail]

See Also

dataMainPlot, dataCustomizedPlot

trvinh/PhyloProfileRibi documentation built on Dec. 23, 2021, 12:57 p.m.