heatmapPlotting {PhyloProfile} | R Documentation |
Create profile heatmap plot
heatmapPlotting(data = NULL, parm = NULL)
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+3) names of 2 variables var1ID and var2ID - default = "var1" & "var2"; (4+5) mid value and color for mid value of var1 - default is 0.5 and #FFFFFF; (6) color for lowest var1 - default = "#FF8C00"; (7) color for highest var1 - default = "#4682B4"; (8+9) mid value and color for mid value of var2 - default is 1 and #FFFFFF;(10) color for lowest var2 - default = "#FFFFFF", (11) color for highest var2 - default = "#F0E68C", (12) color of co-orthologs - default = "#07D000"; (13+14+15) text sizes for x, y axis and legend - default = 9 for each; (16) legend position "top", "bottom", "right", "left" or "none" - default = "top"; (17) zoom ratio of the co-ortholog dots from -1 to 3 - default = 0; (18) angle of x-axis from 0 to 90 - default = 60; (19) show/hide separate line for reference taxon 1/0 - default = 0; (20) enable/disable coloring gene categories TRUE/FALSE - default = FALSE). NOTE: Leave blank or NULL to use default values. |
A profile heatmap plot as a ggplot object.
Vinh Tran tran@bio.uni-frankfurt.de
dataMainPlot
, dataCustomizedPlot
data("superTaxonProfile", package="PhyloProfile") plotDf <- dataMainPlot(superTaxonProfile) plotParameter <- list( "xAxis" = "taxa", "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 ) heatmapPlotting(plotDf, plotParameter)