addRankDivisionPlot: Add taxonomy rank division lines to the heatmap plot

In BIONF/PhyloProfile: PhyloProfile

Add taxonomy rank division lines to the heatmap plot

Description

Add taxonomy rank division lines to the heatmap plot

Usage

addRankDivisionPlot(profilePlot = NULL, plotDf = NULL,
    taxDB = NULL, workingRank = NULL, superRank = NULL, xAxis = "taxa",
    font = "Arial", groupLabelSize = 14, groupLabelDist = 2,
    groupLabelAngle = 90, refLine = TRUE)

Arguments

profilePlot	initial (highlighted) profile plot
plotDf	dataframe for plotting the heatmap phylogentic profile
taxDB	path to taxonomy database (taxonomyMatrix.txt file required!)
workingRank	working taxonomy rank (e.g. species)
superRank	taxonomy rank for division lines (e.g. superkingdom)
xAxis	type of x-axis (either "genes" or "taxa")
font	font of text. Default = Arial"
groupLabelSize	size of rank labels
groupLabelDist	size of the plot area for rank labels
groupLabelAngle	angle of rank labels
refLine	add vertical line to separate reference taxon

Value

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

Author(s)

Vinh Tran [e-mail]

See Also

heatmapPlotting, highlightProfilePlot, getTaxonomyMatrix

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)
workingRank <- "class"
superRank <- "superkingdom"
addRankDivisionPlot(
    profilePlot, plotDf, NULL, workingRank, superRank, "taxa", font = "sans"
)

BIONF/PhyloProfile documentation built on Nov. 7, 2024, 8:31 p.m.