highlightProfilePlot {PhyloProfile} | R Documentation

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

### Description

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

### Usage

    highlightProfilePlot(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 tran@bio.uni-frankfurt.de

### See Also

`dataMainPlot`, `dataCustomizedPlot`

### Examples

    data("fullProcessedProfile", package="PhyloProfile")
    plotDf <- dataMainPlot(fullProcessedProfile)
    plotParameter <- list(
        "xAxis" = "taxa",
        "var1ID" = "FAS_FW",
        "var2ID"  = "FAS_BW",
        "lowColorVar1" =  "#FF8C00",
        "highColorVar1" = "#4682B4",
        "lowColorVar2" = "#FFFFFF",
        "highColorVar2" = "#F0E68C",
        "paraColor" = "#07D000",
        "xSize" = 8,
        "ySize" = 8,
        "legendSize" = 8,
        "mainLegend" = "top",
        "dotZoom" = 0,
        "xAngle" = 60,
        "guideline" = 0,
        "colorByGroup" = FALSE
    )
    taxonHighlight <- "none"
    rankName <- "class"
    geneHighlight <- "100265at6656"
    highlightProfilePlot(
        plotDf, plotParameter, taxonHighlight, rankName, geneHighlight
    )

[Package PhyloProfile version 1.2.8 Index]