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

In BIONF/PhyloProfile: PhyloProfile

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(profilePlot = NULL, plotDf = NULL,
    taxonHighlight = "none", workingRank = "none", geneHighlight = NULL,
    taxDB = NULL, xAxis = "taxa")

Arguments

profilePlot	initial (highlighted) profile plot
plotDf	dataframe for plotting the heatmap phylogentic profile
taxonHighlight	taxon of interst. Default = "none".
workingRank	working taxonomy rank (needed only for highlight taxon).
geneHighlight	gene of interest. Default = NULL.
taxDB	Path to the taxonomy DB files
xAxis	type of x-axis (either "genes" or "taxa")

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, heatmapPlotting

Examples

data("finalProcessedProfile", package="PhyloProfile")
plotDf <- dataMainPlot(finalProcessedProfile)
plotParameter <- list(
    "xAxis" = "taxa",
    "geneIdType" = "geneID",
    "var1ID" = "FAS_FW",
    "var2ID"  = "FAS_BW",
    "midVar1" = 0.5,
    "midColorVar1" =  "#FFFFFF",
    "lowColorVar1" =  "#FF8C00",
    "highColorVar1" = "#4682B4",
    "midVar2" = 1,
    "midColorVar2" =  "#FFFFFF",
    "lowColorVar2" = "#CB4C4E",
    "highColorVar2" = "#3E436F",
    "paraColor" = "#07D000",
    "xSize" = 8,
    "ySize" = 8,
    "legendSize" = 8,
    "mainLegend" = "top",
    "dotZoom" = 0,
    "xAngle" = 60,
    "guideline" = 0,
    "colorByGroup" = FALSE,
    "colorByOrthoID" = FALSE
)
profilePlot <- heatmapPlotting(plotDf, plotParameter)
taxonHighlight <- "none"
workingRank <- "class"
geneHighlight <- "100265at6656"
highlightProfilePlot(
    profilePlot, plotDf, taxonHighlight, workingRank, geneHighlight,
    NULL, plotParameter$xAxis
)

BIONF/PhyloProfile documentation built on Dec. 18, 2024, 7:33 a.m.