draw_sunburst_wt_fill: Draw sunburst plot showing MEGENA module hierarchy.

In MEGENA: Multiscale Clustering of Geometrical Network

Description

Sunburst plot and colored heatmaps

Usage

  draw_sunburst_wt_fill(module.df,
                        parent.col = "module.parent",id.col = "id",
                        min.angle = 5,
                        feat.col,
                        fill.type = "continuous",log.transform = TRUE,
                        fill.scale = NULL,
                        theme.adjust = NULL
                        )

Arguments

module.df	A data.frame table summarizing module information. Must contain module parent and child relation for hierarchy visualization.
parent.col	Character object, name for the parent module column in module.df.
id.col	Character object for the module id column in module df.
min.angle	Minimum angle that rectangles in the sunburst are labeled with respective module id.
feat.col	Chracter object, for the feature column in module.df to color the heatmaps.
fill.type	continuous/discrete, is the variable numeric (continuous) or factor (discrete)?
log.transform	TRUE/FALSE. do log10 transform for p-values?
fill.scale	A ggplot object to specify heatmap coloring scheme. Permissible functions are: scale_fill_gradient,scale_fill_gradient2,scale_fill_gradientn,scale_fill_manual.
theme.adjust	A ggplot object to specify theme for plotting.

Details

makes use of ggraph scheme to manipulate and draw sunburst plot in ggplot2 framework. fill.scale and theme.adjust provide flexibility to designate heatmap coloring schemes and figure aesthetics.

Value

ggplot object for the figure

Author(s)

Won-Min Song

Examples

  ## Not run: 
    rm(list = ls())
    data(Sample_Expression)
    ijw <- calculate.correlation(datExpr[1:100,],doPerm = 2)
    el <- calculate.PFN(ijw[,1:3])
    g <- graph.data.frame(el,directed = FALSE)
    MEGENA.output <- do.MEGENA(g = g,remove.unsig = FALSE,doPar = FALSE,n.perm = 10)
    output.summary <- MEGENA.ModuleSummary(MEGENA.output,
    mod.pvalue = 0.05,hub.pvalue = 0.05,
    min.size = 10,max.size = 5000,
    annot.table = NULL,id.col = NULL,symbol.col = NULL,
    output.sig = TRUE)
    
    # no coloring 
    sbobj = draw_sunburst_wt_fill(module.df = output.summary$module.table,
    feat.col = NULL,id.col = "module.id",parent.col = "module.parent")
    sbobj
    
    # get some coloring (with log transform option)
    mdf= output.summary$module.table
    mdf$heat.pvalue = runif(nrow(mdf),0,0.1)
    
    sbobj = draw_sunburst_wt_fill(module.df = mdf,feat.col = "heat.pvalue",log.transform = TRUE,
    fill.type = "continuous",
    fill.scale = scale_fill_gradient2(low = "white",mid = "white",high = "red",
    midpoint = -log10(0.05),na.value = "white"), 
    id.col = "module.id",parent.col = "module.parent")
    sbobj
    
    # get discrete coloring done
    mdf$category = factor(sample(x = c("A","B"),size = nrow(mdf),replace = TRUE))
    sbobj = draw_sunburst_wt_fill(module.df = mdf,feat.col = "category",
    fill.type = "discrete",
    fill.scale = scale_fill_manual(values = c("A" = "red","B" = "blue")), 
    id.col = "module.id",parent.col = "module.parent")
    sbobj
  
## End(Not run)

MEGENA documentation built on May 1, 2019, 8:07 p.m.