ggheat.continuous.single
ggheatmap function for plotting a single esetR/ggheat.continuous.R
ggheat.continuous.single.Rd
ggheat.continuous.single
ggheatmap function for plotting a single eset
ggheat.continuous.single( eset, hc, hr, hmcolors = NA, hmtitle = "expression", col_lab, col_legend, ylabstr = "", fout = NA, p.heights = c(1.5, 0.5, 5), xsize = 4, ysize = 4, ysizelab = 7, xright = 0.24, override.hc = NA )
eset | expression set |
---|---|
hc | column clustering from hclust or hcopt |
hr | 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) |
xright | default 0.24, displayed width for right margin as fraction of whole plot width |