R/diamondCoordinates.R, R/ggDiamondLayer.R, R/rawDataDiamondLayer.R, and 1 more
basicDiamondplotFunctions.RdThese functions are used by diamondPlot() to construct a diamond
plot. It's normally not necessary to call this function directly: instead,
use meansDiamondPlot(), meanSDtoDiamondPlot(), and
factorLoadingDiamondCIplot().
diamondCoordinates(
values,
otherAxisValue = 1,
direction = "horizontal",
autoSize = NULL,
fixedSize = 0.15
)
ggDiamondLayer(
data,
ciCols = 1:3,
colorCol = NULL,
generateColors = NULL,
fullColorRange = NULL,
color = "black",
lineColor = NA,
otherAxisCol = 1:nrow(data),
autoSize = NULL,
fixedSize = 0.15,
direction = "horizontal",
...
)
rawDataDiamondLayer(
dat,
items = NULL,
itemOrder = 1:length(items),
dataAlpha = 0.1,
dataColor = "#444444",
jitterWidth = 0.5,
jitterHeight = 0.4,
size = 3,
...
)
varsToDiamondPlotDf(
dat,
items = NULL,
labels = NULL,
decreasing = NULL,
conf.level = 0.95
)A vector of 2 or more values that are used to construct the diamond coordinates. If three values are provided, the middle one becomes the diamond's center. If two, four, or more values are provided, the median becomes the diamond's center.
The value on the other axis to use to compute the
coordinates; this will be the Y axis value of the points of the diamond (if
direction is 'horizontal') or the X axis value (if direction
is 'vertical').
Whether the diamonds should be constructed horizontally or vertically.
Whether to make the height of each diamond conditional upon its length (the width of the confidence interval).
If not using relative heights, fixedSize determines
the height to use.
A dataframe (or matrix) containing lower bounds, centers
(e.g. means), and upper bounds of intervals (e.g. confidence intervals) for
ggDiamondLayer or items and raw data for varsToDiamondPlotDf
and rawDataDiamondLayer.
The columns in the dataframe with the lower bounds, centers (e.g. means), and upper bounds (in that order).
The column in the dataframe containing the colors for each diamond, or a vector with colors (with as many elements as the dataframe has rows).
A vector with colors to use to generate a gradient.
These colors must be valid arguments to colorRamp() (and
therefore, to col2rgb()).
When specifying a gradient using
generateColors, it is usually desirable to specify the minimum and
maximum possible value corresponding to the outer anchors of that gradient.
For example, when plotting numbers from 0 to 100 using a gradient from 'red'
through 'orange' to 'green', none of the means may actually be 0 or 100; the
lowest mean may be, for example, 50. If no fullColorRange is
specified, the diamond representing that lowest mean of 50 wil be red, not
orange. When specifying the fullColorRange, the lowest and highest
'colors' in generateColors are anchored to the minimum and maximum
values of fullColorRange.
When no colors are automatically generated, all diamonds will have this color.
If NA, lines will have the same colors as the diamonds'
fill. If not NA, must be a valid color, which is then used as line color.
Note that e.g. linetype and color can be used as well, which
will be passed on to geom_polygon().
A vector of values, or the index of the column in the dataframe, that specifies the values for the Y axis of the diamonds. This should normally just be a vector of consecutive integers.
Any additional arguments are passed to
geom_polygon(). This can be used to set, for example, the
alpha value of the diamonds. Additional arguments for
rawDataDiamondLayer are passed on to geom_jitter().
The items from the dataframe to include in the diamondplot or dataframe.
Order of the items to use (if not sorting).
This determines the alpha (transparency) of the data points.
The color of the data points.
How much to jitter the individual datapoints horizontally.
How much to jitter the individual datapoints vertically.
The size of the data points.
The item labels to add to the dataframe.
Whether to sort the items (rows) in the dataframe decreasing (TRUE), increasing (FALSE), or not at all (NULL).
The confidence of the confidence intervals.
ggDiamondLayer returns a ggplot()
geom_polygon() object, which can then be used in
ggplot() plots (as diamondPlot() does).
diamondCoordinates returns a set of four coordinates that together
specify a diamond.
varsToDiamondPlotDf returns a dataframe of diamondCoordinates.
rawDataDiamondLayer returns a geom_jitter() object.
if (FALSE) {
### (Don't run this example as a test, because we
### need the ggplot function which isn't part of
### this package.)
### The coordinates for a simple diamond
diamondCoordinates(values = c(1,2,3));
### Plot this diamond
ggplot() + ggDiamondLayer(data.frame(1,2,3));
}