heatmapPlotting: Create profile heatmap plot

In BIONF/PhyloProfile: PhyloProfile

Create profile heatmap plot

Description

Create profile heatmap plot

Usage

heatmapPlotting(data = NULL, parm = NULL)

Arguments

data

dataframe for plotting the heatmap phylogentic profile (either full or subset profiles)

parm

plot parameters, including (1) type of x-axis "taxa" or "genes" - default = "taxa"; (2) display gene IDs (default) or gene names; (3+4) names of 2 variables var1ID and var2ID - default = "var1" & "var2"; (5+6) mid value and color for mid value of var1 - default is 0.5 and #FFFFFF; (7) color for lowest var1 - default = "#FF8C00"; (8) color for highest var1 - default = "#4682B4"; (9+10) mid value and color for mid value of var2 - default is 1 and #FFFFFF;(11) color for lowest var2 - default = "#FFFFFF", (12) color for highest var2 - default = "#F0E68C", (13) color of co-orthologs - default = "#07D000"; (14+15+16) text sizes for x, y axis and legend - default = 9 for each; (17) legend position "top", "bottom", "right", "left" or "none" - default = "top"; (18) zoom ratio of the co-ortholog dots from -1 to 3 - default = 0; (19) angle of x-axis from 0 to 90 - default = 60; (20) show/hide separate line for reference taxon 1/0 - default = 0; (21) enable/disable coloring gene categories TRUE/FALSE - default = FALSE; (22) enable/disable coloring duplicated ortholog IDs TRUE/FALSE - default=FALSE). NOTE: Leave blank or NULL to use default values.

Value

A profile heatmap plot as a ggplot object.

Author(s)

Vinh Tran [e-mail]

See Also

dataMainPlot, dataCustomizedPlot

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,
    "catColors" = NULL,
    "colorByOrthoID" = FALSE
)

heatmapPlotting(plotDf, plotParameter)

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