picketplot {Heatplus} | R Documentation |
Display one or more binary variables by using black bars for presence/validity of a condition, empty space for absence/invalidity, and an extra color for missing values. Additionally, an index plot for one interval scaled variable can be added, possibly with a smoothing function.
This routine is primarily intended for augmenting heatmaps. It might be useful in other contexts, but misses most frills for using it comfortably.
picketplot(x, covariate = NULL, grp = NULL, grpcol, grplabel = NULL, add = FALSE, control = list())
x |
a matrix or data frame containing the data. |
covariate |
the index of the column in x that contains the interval scaled variable, if any. |
grp |
cluster indices for the rows of x , used for assigning background color. |
grpcol |
colors corresponding to the clusters. |
grplabel |
cluster names. |
add |
logical indicating whether to start a new plot, or whether to add the plot to the existing one. |
control |
a list of parameters controlling the appearance of the plot, see Details. |
The following named list elements can be set to change the appearance of the plot:
loess
used for the smoothing curve.loess
used for
the smoothing curve.grplabel
.The plot looks like a more or less derelict picket fence, and 'picketplot' sounds somewhat like the 'pocketplot' used in geostatistics.
Alexander Ploner <Alexander.Ploner@ki.se>
# without covariate mm = cbind(sample(0:1, 42, rep=TRUE), sample(0:1, 42, rep=TRUE)) mm[sample(42, 5), 1] = NA picketplot(mm) # with clustering cl = rep(1:3, c(10,22,10)) cn = c("Cluster I","Cluster II","Cluster III") cc = c("lightblue","lightgreen","lightpink") # windows palette picketplot(mm, grp=cl, grplabel=cn, grpcol=cc) # add a covariate; setting the colnames makes the variable labels mm = cbind(mm, rnorm(42) + cl/2) colnames(mm) = c("State A","State B", "X") picketplot(mm, covariate=3,grp=cl, grplabel=cn, grpcol=cc) # using extra controls picketplot(mm, covariate=3,grp=cl, grplabel=cn, grpcol=cc, control=list(nacol="white", degree=0))