ggheat.continuous.group ggheatmap function for plotting groups of esets, within-group column clustering

ggheat.continuous.group ggheatmap function for plotting groups of esets, within-group column clustering

ggheat.continuous.group(
  esetlist,
  hclist,
  hrlist,
  hmcolors,
  hmtitle = "expression",
  col_lab,
  col_legend,
  ylabstr = "",
  fout,
  p.heights = c(1.5, 0.5, 5),
  xsize = 4,
  ysize = 4,
  ysizelab = 7,
  xleft = 0.15,
  xright = 0.24
)

Arguments

esetlist	list of expression sets, see ?heatmap.make.groups for preprocessing
hclist	list of column clustering from hclust or hcopt
hrlist	list of row clustering from hclust or hcopt
hmcolors	function for heatmap color gradient, default: hmcolors<-function(... ) scale_fill_gradient2(low = "blue", mid = "white", high = "red", midpoint = 0, limits=c(-3,3), oob=squish, ...)
hmtitle	title of heatmap color label, default: "expression"
col_lab	column color label to display, one or more of columns of pData(eset)
col_legend	named list of column color legends, names correspond to col_lab, see format: col_legend<-list(COL1 = list(col_breaks = COL1levels, col_values = brewer.pal(length(COL1levels),"Set1"), col_labels = COL1levels), COL2 = list(col_breaks = COL2levels, col_values = brewer.pal(length(COL2levels),"Set2"), col_labels = COL2levels))
ylabstr	y axis title string,
fout	filename to save plot, default NA, save as object, to display to device, use grid.arrange
p.heights	panel heights default c(1.5, 0.5, 5),
xsize	default 4 x axis labels (uses colnames), set to 0 to turn off display
ysize	default 4, y axis labels (uses rownames), set to 0 to turn off display
ysizelab	default 7, text size for y axis title (specified in ylabstr)
xleft	default 0.15, displayed width for left panel + margin as fraction of whole plot width
xright	default 0.24, displayed width for right margin as fraction of whole plot width

Examples

data(tcga.subset.400g.200s)
#> Warning: data set ‘tcga.subset.400g.200s’ not found
dat
#> Error in eval(expr, envir, enclos): object 'dat' not found

subtypelevels<-levels(dat$subtype)
#> Error in levels(dat$subtype): object 'dat' not found

grps<-ggheat.make.groups(eset = dat,
  labelcol = "subtype",  #column name for grouping in pData(eset)
  labelvals = subtypelevels, #values to group on (e.g. factor levels of pData(eset)[, labelcol])
  clustFUN = clust_eset #clustering function for eset
  )
#> Error in is.data.frame(x): object 'dat' not found

col_legend<-list(subtype = list(col_breaks = subtypelevels,
    col_values = brewer.pal(length(subtypelevels),"Set1"),
    col_labels = subtypelevels))
#> Error in eval(expr, envir, enclos): object 'subtypelevels' not found

esetlist<-lapply(grps$esetlist, function(i) scale_row(i))
#> Error in lapply(grps$esetlist, function(i) scale_row(i)): object 'grps' not found

hmcolors<-function(... ) scale_fill_gradient2(low = "blue", mid = "white",
       high = "red", midpoint = 0, limits=c(-3,3), oob=squish, ...)

p<-ggheat.continuous.group(esetlist,
  grps$hclist,
  grps$hrlist,
  hmcolors,
  hmtitle = "row-zscore GE",
  col_lab = "subtype",
  col_legend = col_legend,
  ylabstr = "",
  fout  = NA,
  p.heights = c(1.5, 0.5, 5),
  xsize = 0,
  ysize = 0,
  ysizelab = 7,
  xleft = 0.10,
  xright = 0.24)
#> Error in ggheat.continuous.group(esetlist, grps$hclist, grps$hrlist, hmcolors,     hmtitle = "row-zscore GE", col_lab = "subtype", col_legend = col_legend,     ylabstr = "", fout = NA, p.heights = c(1.5, 0.5, 5), xsize = 0,     ysize = 0, ysizelab = 7, xleft = 0.1, xright = 0.24): object 'esetlist' not found