HiveR (version 0.4.0)

HidingAnAxis: How to Hide An Axis in a Hive Plot, with Bonus 2 Plots on One Page

Description

From time-to-time is useful to compare several hive plots based on related data (and you might wish to plot them side-by-side to facilitate comparison). Depending the nature of the data set and how it changes under the experimental design, some data sets may not have any nodes on a particular axis (and therefore, they don't participate in edges either). Let's say your system fundamentally has three axes, but in some data sets one of the axes has no nodes. When you plot them side-by-side, for visual comparison it is nice if all the plots, including the one with an empty axis, have the same general orientation. In other words, even if the data only requires two axes, you might want it plotted as if it had three axes for consistency in overall appearance.

Author

Bryan A. Hanson, DePauw University.

Details

When an axis is present but doesn't have a node on it, this makes plotHive unhappy, but there is a simple solution. You simply put a dummy or phantom node on the empty axis. This is illustrated in the example below. Also demonstrated is a simple grid-based function for putting more than one plot on a device.

Examples

require("grid")

# Adjacency matrix describing the connectivity in 2-butanone
# H's on a single carbon collapsed into a group.
# Matrix entry is bond order.  CH3 is coded so the
# bond order between C & H is 3 (3 single C-H bonds)

dnames <- c("C1", "C2", "C3", "C4", "O", "HC1", "HC3", "HC4")

#                    C1, C2, C3, C4, O, HC1, HC3, HC4
butanone <- matrix(c(
  0, 1, 0, 0, 0, 3, 0, 0, # C1
  1, 0, 1, 0, 2, 0, 0, 0, # C2
  0, 1, 0, 1, 0, 0, 2, 0, # C3
  0, 0, 1, 0, 0, 0, 0, 3, # C4
  0, 2, 0, 0, 0, 0, 0, 0, # O
  3, 0, 0, 0, 0, 0, 0, 0, # HC1
  0, 0, 2, 0, 0, 0, 0, 0, # HC3
  0, 0, 0, 3, 0, 0, 0, 0
), # HC4
ncol = 8, byrow = TRUE,
dimnames = list(dnames, dnames)
)

butanoneHPD <- adj2HPD(
  M = butanone, axis.col = c("black", "gray", "red"),
  desc = "2-butanone"
)

# Fix up the nodes manually (carbon is on axis 1)
butanoneHPD$nodes$axis[5] <- 3L # oxygen on axis 3
butanoneHPD$nodes$axis[6:8] <- 2L # hydrogen on axis 2
butanoneHPD$nodes$color[5] <- "red"
butanoneHPD$nodes$color[6:8] <- "gray"

# Exaggerate the edge weights, which are proportional to the number of bonds
butanoneHPD$edges$weight <- butanoneHPD$edges$weight^2
butanoneHPD$edges$color <- rep("wheat3", 7)

plotHive(butanoneHPD,
  method = "rank", bkgnd = "white",
  axLabs = c("carbon", "hydrogen", "oxygen"),
  axLab.pos = c(1, 1, 1), axLab.gpar =
    gpar(col = c("black", "gray", "red"))
)

# Now repeat the process for butane

dnames <- c("C1", "C2", "C3", "C4", "HC1", "HC2", "HC3", "HC4")

#                  C1, C2, C3, C4, HC1, HC2, HC3, HC4
butane <- matrix(c(
  0, 1, 0, 0, 3, 0, 0, 0, # C1
  1, 0, 1, 0, 0, 2, 0, 0, # C2
  0, 1, 0, 1, 0, 0, 2, 0, # C3
  0, 0, 1, 0, 0, 0, 0, 3, # C4
  3, 0, 0, 0, 0, 0, 0, 0, # HC1
  0, 2, 0, 0, 0, 0, 0, 0, # HC2
  0, 0, 2, 0, 0, 0, 0, 0, # HC3
  0, 0, 0, 3, 0, 0, 0, 0
), # HC4
ncol = 8, byrow = TRUE,
dimnames = list(dnames, dnames)
)

butaneHPD <- adj2HPD(
  M = butane, axis.col = c("black", "gray"),
  desc = "butane"
)
butaneHPD$nodes$axis[5:8] <- 2L # hydrogen on axis 2
butaneHPD$nodes$color[5:8] <- "gray"
butaneHPD$edges$weight <- butaneHPD$edges$weight^2
butaneHPD$edges$color <- rep("wheat3", 7)

plotHive(butaneHPD,
  method = "rank", bkgnd = "white",
  axLabs = c("carbon", "hydrogen"),
  axLab.pos = c(1, 1), axLab.gpar = gpar(col = c("black", "gray"))
)

# butaneHPD has 2 axes.  If we wanted to compare to butanoneHPD effectively
# we should add a third dummy axis where the oxygen axis was in butanone
# You might want to look at str(butaneHPD) before beginning

dummy <- c(9, "dummy", 3, 1.0, 1.0, "white") # mixed data types
# but coerced to character
butaneHPD$nodes <- rbind(butaneHPD$nodes, dummy)
str(butaneHPD$nodes) # The data types are mangled from the rbind!

# Now coerce the data types to the standard of the class, and check it
butaneHPD$nodes$id <- as.integer(butaneHPD$nodes$id)
butaneHPD$nodes$axis <- as.integer(butaneHPD$nodes$axis)
butaneHPD$nodes$radius <- as.numeric(butaneHPD$nodes$radius)
butaneHPD$nodes$size <- as.numeric(butaneHPD$nodes$size)
str(butaneHPD$nodes)

chkHPD(butaneHPD) # OK! (False means there were no problems)
sumHPD(butaneHPD)

# Plot it

plotHive(butaneHPD,
  method = "rank", bkgnd = "white",
  axLabs = c("carbon", "hydrogen", "oxygen"),
  axLab.pos = c(1, 1, 1), axLab.gpar =
    gpar(col = c("black", "gray", "red"))
)

# Put 2 plots side-by-side using a little helper function

vplayout <- function(x, y) viewport(layout.pos.row = x, layout.pos.col = y)

# pdf("Demo.pdf", width = 10, height = 5) # Aspect ratio better
# default screen device

grid.newpage()
pushViewport(viewport(layout = grid.layout(1, 2)))
pushViewport(vplayout(1, 1)) # left plot

plotHive(butanoneHPD,
  method = "rank", bkgnd = "white",
  axLabs = c("carbon", "hydrogen", "oxygen"),
  axLab.pos = c(1, 1, 1), axLab.gpar =
    gpar(col = c("black", "gray", "red")), np = FALSE
)
grid.text("butanone",
  x = 0.5, y = 0.1, default.units = "npc",
  gp = gpar(fontsize = 14, col = "black")
)

popViewport(2)
pushViewport(vplayout(1, 2)) # right plot
grid.text("test2")

plotHive(butaneHPD,
  method = "rank", bkgnd = "white",
  axLabs = c("carbon", "hydrogen", "oxygen"),
  axLab.pos = c(1, 1, 1), axLab.gpar =
    gpar(col = c("black", "gray", "red")), np = FALSE
)
grid.text("butane",
  x = 0.5, y = 0.1, default.units = "npc",
  gp = gpar(fontsize = 14, col = "black")
)

# dev.off()