- x
a vector of numeric data, or a data frame (for jitter2 or
ecdfpM)
- object
a data frame or list (even with unequal number of observations per
variable, as long as group is notspecified)
- side
axis side to use (1=bottom (default for histSpike), 2=left,
3=top (default for scat1d), 4=right)
- frac
fraction of smaller of vertical and horizontal axes for tick mark
lengths. Can be negative to move tick marks outside of plot. For
histSpike, this is the relative y-direction length to be used for the
largest frequency. When scat1d calls histSpike, it
multiplies its frac argument by 2.5. For histSpikeg,
frac is a function of f, the vector of all frequencies. The
default function scales tick marks so that they are between 0.01 and
0.03 of the y range, linearly scaled in the square root of the
frequency less one.
- jitfrac
fraction of axis for jittering. If
\(\code{jitfrac} \le 0\), no
jittering is done. If preserve=TRUE, the amount of
jittering is independent of jitfrac.
- tfrac
Fraction of tick mark to actually draw. If \(\code{tfrac}<1\),
will draw a random fraction tfrac of the line segment at
each point. This is useful for very large samples or ones with some
very dense points. The default value is 1 if the number of
non-missing observations n is less than 125, and
\(\max{(.1, 125/n)}\) otherwise.
- eps
fraction of axis for determining overlapping points in x. For
preserve=TRUE the default is 0 and original unique values are
retained, bigger values of eps tends to bias observations from dense
to sparse regions, but ranks are still preserved.
- lwd
line width for tick marks, passed to segments
- col
color for tick marks, passed to segments
- y
specify a vector the same length as x to draw tick marks
along a curve instead of by one of the axes. The y values
are often predicted values from a model. The side argument
is ignored when y is given. If the curve is already
represented as a table look-up, you may specify it using the
curve argument instead. y may be a scalar to use a
constant verticalplacement.
- curve
a list containing elements x and y for which linear
interpolation is used to derive y values corresponding to
values of x. This results in tick marks being drawn along
the curve. For histSpike, interpolated y values are
derived for binmidpoints.
- minimal
for histSpike set minimal=TRUE to draw a
minimalist spike histogram with no y-axis. This works best when
produce graphics images that are short, e.g., have a height of
two inches. add is forced to be FALSE in this case
so that a standalone graph is produced. Only base graphics are
used.
- bottom.align
set to TRUE to have the bottoms of tick marks (for
side=1 or side=3) aligned at the y-coordinate. The
default behavior is to center the tick marks. For
datadensity.data.frame, bottom.align defaults to
TRUE if nint>1. In other words, if you are only
labeling the first and last axis tick mark, the scat1d tick
marks are centered on the variable's axis.
- preserve
set to TRUE to invoke jitter2
- fill
maximum fraction of the axis filled by jittered values. If d
are duplicated values between a lower value l and upper value
u, then d will be spread within
\(\pm \code{fill}*\min{(u-d,d-l)}/2\).
- limit
specifies a limit for maximum shift in jittered values. Duplicate
values will be spread within
\(\pm\code{fill}*\min{(u-d,d-l)}/2\). The
default TRUE restricts jittering to the smallest
\(\min{(u-d,d-l)}/2\) observed and results
in equal amount of jittering for all d. Setting to
FALSE allows for locally different amount of jittering, using
maximum space available.
- nhistSpike
If the number of observations exceeds or equals nhistSpike,
scat1d will automatically call histSpike to draw the
data density, to prevent the graphics file from being too large.
- type
used by or passed to histSpike. Set to "count" to
display frequency counts rather than relative frequencies, or
"density" to display a kernel density estimate computed using
the density function.
- grid
set to TRUE if the R grid package is in effect for
the current plot
- nint
number of intervals to divide each continuous variable's axis for
datadensity. For histSpike, is the number of
equal-width intervals for which to bin x, and if instead
nint is a character string (e.g.,nint="all"), the
frequency tabulation is done with no binning. In other words,
frequencies for all unique values of x are derived and
plotted. For histSpikeg, if x has no more than
nint unique values, all observed values are used, otherwise
the data are rounded before tabulation so that there are no more
than nint intervals. For histSpike, nint is
ignored if bins is given.
- bins
for histSpike specifies the actual cutpoints to use
for binning x. The default is to use nint in
conjunction with xlim.
- ...
optional arguments passed to scat1d from datadensity
or to histSpike from scat1d. For histSpikep
are passed to the lines list to add_trace. For
ecdfpM these arguments are passed to add_lines.
- presorted
set to TRUE to prevent from sorting for determining the order
\(l<d<u\). This is usefull if an existing
meaningfull local order would be destroyed by sorting, as in
\(\sin{(\pi*\code{sort}(\code{round}(\code{runif}(1000,0,10),1)))}\).
- group
an optional stratification variable, which is converted to a
factor vector if it is not one already
- which
set which="continuous" to only plot continuous variables, or
which="categorical" to only plot categorical, character, or
discrete numeric ones. By default, all types of variables are
depicted.
- method.cat
set method.cat="freq" to depict frequencies of categorical
variables with digits representing the cell frequencies, with size
proportional to the square root of the frequency. By default,
vertical bars are used.
- col.group
colors representing the group strata. The vector of colors
is recycled to be the same length as the levels of group.
- n.unique
number of unique values a numeric variable must have before it is
considered to be a continuous variable
- show.na
set to FALSE to suppress drawing the number of NAs to
the right of each axis
- naxes
number of axes to draw on each page before starting a new plot. You
can set naxes larger than the number of variables in the data
frame if you want to compress the plot vertically.
- q
a vector of quantiles to display. By default, quantiles are not
shown.
- extra
a two-vector specifying the fraction of the x
range to add on the left and the fraction to add on the right
- cex.axis
character size for draw labels for axis tick marks
- cex.var
character size for variable names and frequence of NAs
- lmgp
spacing between numeric axis labels and axis (see par for
mgp)
- tck
see tck under par
- ranges
a list containing ranges for some or all of the numeric variables.
If ranges is not given or if a certain variable is not found
in the list, the empirical range, modified by pretty, is
used. Example:
ranges=list(age=c(10,100), pressure=c(50,150)).
- labels
a vector of labels to use in labeling the axes for
datadensity.data.frame. Default is to use the names of the
variable in the input data frame. Note: margin widths computed for
setting aside names of variables use the names, and not these
labels.
- minf
For histSpike, if minf is specified low bin
frequencies are set to a minimum value of minf times the
maximum bin frequency, so that rare data points will remain visible.
A good choice of minf is 0.075.
datadensity.data.frame passes minf=0.075 to
scat1d to pass to histSpike. Note that specifying
minf will cause the shape of the histogram to be distorted
somewhat.
- mult.width
multiplier for the smoothing window width computed by
histSpike when type="density"
- xlim
a 2-vector specifying the outer limits of x for binning (and
plotting, if add=FALSE and nint is a number). For
histSpikeg, observations outside the xlim range are ignored.
- ylim
y-axis range for plotting (if add=FALSE). Often needed for
histSpikeg to help scale the tick mark line segments.
- xlab
x-axis label (add=FALSE or for ecdfpM); default is
name of input argument, or for ecdfpM comes from
label and units attributes of the analysis
variable. For ecdfpM xlab may be a vector if there
is more than one analysis variable.
- ylab
y-axis label (add=FALSE or for ecdfpM)
- add
set to TRUE to add the spike-histogram to an existing plot,
to show marginal data densities
- formula
a formula of the form y ~ x1 or y ~ x1 + ... where
y is the name of the y-axis variable being plotted
with ggplot, x1 is the name of the x-axis
variable, and optional ... are variables used by
ggplot to produce multiple curves on a panel and/or facets.
- predictions
the data frame being plotted by ggplot, containing x
and y coordinates of curves. If omitted, spike histograms
are drawn at the bottom (default) or top of the plot according to
side.
- data
for histSpikeg is a mandatory data frame containing raw data whose
frequency distribution is to be summarized, using variables in
formula.
- plotly
an existing plotly object. If not NULL,
histSpikeg uses plotly instead of ggplot.
- lowess
set to TRUE to have histSpikeg add a geom_line
layer to the ggplot2 graphic, containing
lowess() nonparametric smoothers. This causes the
returned value of histSpikeg to be a list with two
components: "hist" and "lowess" each containing
a layer. Fortunately, ggplot2 plots both layers
automatically. If the dependent variable is binary,
iter=0 is passed to lowess so that outlier
detection is turned off; otherwise iter=3 is passed.
- span
passed to lowess as the f argument
- histcol
color of line segments (tick marks) for
histSpikeg. Default is black. Set to any color or to
"default" to use the prevailing colors for the
graphic.
- showlegend
set to FALSE too have the added plotly
traces not have entries in the plot legend
- what
set to "1-F" to plot 1 minus the ECDF instead of the
ECDF, "f" to plot cumulative frequency, or "1-f" to
plot the inverse cumulative frequency
- height,width
passed to plot_ly
- colors
a vector of colors to pas to add_lines
- nrows,ncols
passed to plotly::subplot