aggregate hyperSpec objects
Compute summary statistics for subsets of a hyperSpec object.
## S4 method for signature 'hyperSpec'
aggregate(
x,
by = stop("by is needed"),
FUN = stop("FUN is needed."),
...,
out.rows = NULL,
append.rows = NULL,
by.isindex = FALSE
)x |
a |
by |
grouping for the rows of Either a list containing an index vector for each of the subgroups or a
vector that can be |
FUN |
function to compute the summary statistics |
... |
further arguments passed to |
out.rows |
number of rows in the resulting |
append.rows |
If more rows are needed, how many should be appended? Defaults to 100 or an estimate based on the percentage of groups that are still to be done, whatever is larger. |
by.isindex |
If a list is given in |
aggregate avoids splitting x@data.
FUN does not need to return exactly one value. The number of
returned values needs to be the same for all wavelengths (otherwise the
result could not be a matrix), see the examples.
If the initially preallocated data.frame turns out to be too small,
more rows are appended and a warning is issued.
A hyperSpec object with an additional column
@data$.aggregate tracing which group the rows belong to.
C. Beleites
cluster.means <- aggregate (chondro, chondro$clusters, mean_pm_sd)
plot(cluster.means, stacked = ".aggregate", fill = ".aggregate",
col = matlab.dark.palette (3))
## make some "spectra"
spc <- new ("hyperSpec", spc = sweep (matrix (rnorm (10*20), ncol = 20), 1, (1:10)*5, "+"))
## 3 groups
color <- c("red", "blue", "black")
by <- as.factor (c (1, 1, 1, 1, 1, 1, 5, 1, 2, 2))
by
plot (spc, "spc", col = color[by])
## Example 1: plot the mean of the groups
plot (aggregate (spc, by, mean), "spc", col = color, add = TRUE,
lines.args = list(lwd = 3, lty = 2))
## Example 2: FUN may return more than one value (here: 3)
plot (aggregate (spc, by, mean_pm_sd), "spc",
col = rep(color, each = 3), lines.args = list(lwd = 3, lty = 2))
## Example 3: aggregate even takes FUN that return different numbers of
## values for different groups
plot (spc, "spc", col = color[by])
weird.function <- function (x){
if (length (x) == 1)
x + 1 : 10
else if (length (x) == 2)
NULL
else
x [1]
}
agg <- aggregate (spc, by, weird.function)
agg$.aggregate
plot (agg, "spc", add = TRUE, col = color[agg$.aggregate],
lines.args = list (lwd = 3, lty = 2))Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.