Plots the event data and estimated CMA encapsulated in objects derived from
CMA0.
# S3 method for CMA1
plot(x, ..., patients.to.plot = NULL, duration = NA,
align.all.patients = FALSE, align.first.event.at.zero = TRUE,
show.period = c("dates", "days")[2], period.in.days = 90,
show.legend = TRUE, legend.x = "right", legend.y = "bottom",
legend.bkg.opacity = 0.5, legend.cex = 0.75, legend.cex.title = 1,
cex = 1, cex.axis = 0.75, cex.lab = 1, show.cma = TRUE,
col.cats = rainbow, unspecified.category.label = "drug",
lty.event = "solid", lwd.event = 2, pch.start.event = 15,
pch.end.event = 16, show.event.intervals = TRUE,
col.na = "lightgray", print.CMA = TRUE, CMA.cex = 0.5,
plot.CMA = TRUE, CMA.plot.ratio = 0.1, CMA.plot.col = "lightgreen",
CMA.plot.border = "darkgreen", CMA.plot.bkg = "aquamarine",
CMA.plot.text = CMA.plot.border, highlight.followup.window = TRUE,
followup.window.col = "green", highlight.observation.window = TRUE,
observation.window.col = "yellow", observation.window.density = 35,
observation.window.angle = -30, observation.window.opacity = 0.3,
show.real.obs.window.start = TRUE, real.obs.window.density = 35,
real.obs.window.angle = 30, print.dose = FALSE, cex.dose = 0.75,
print.dose.outline.col = "white", print.dose.centered = FALSE,
plot.dose = FALSE, lwd.event.max.dose = 8,
plot.dose.lwd.across.medication.classes = FALSE, bw.plot = FALSE,
min.plot.size.in.characters.horiz = 10,
min.plot.size.in.characters.vert = 0.5, max.patients.to.plot = 100)# S3 method for CMA2
plot(...)
# S3 method for CMA3
plot(...)
# S3 method for CMA4
plot(...)
# S3 method for CMA5
plot(...)
# S3 method for CMA6
plot(...)
# S3 method for CMA7
plot(...)
# S3 method for CMA8
plot(...)
# S3 method for CMA9
plot(...)
A CMA0 or derived object, representing the CMA to
plot
other possible parameters
A vector of strings containing the list of
patient IDs to plot (a subset of those in the cma object), or
NULL for all
A number, the total duration (in days) of the whole
period to plot; in NA it is automatically determined from the event
data such that the whole dataset fits.
Logical, should all patients be aligned (i.e., the actual dates are discarded and all plots are relative to the earliest date)?
Logical, should the first event be placed at the origin of the time axis (at 0)?
A string, if "dates" show the actual dates at the
regular grid intervals, while for "days" (the default) shows the days since
the beginning; if align.all.patients == TRUE, show.period is
taken as "days".
The number of days at which the regular grid is drawn (or 0 for no grid).
Logical, should the legend be drawn?
The position of the legend on the x axis; can be "left", "right" (default), or a numeric value.
The position of the legend on the y axis; can be "bottom" (default), "top", or a numeric value.
A number between 0.0 and 1.0 specifying the opacity of the legend background.
numeric
values specifying the cex of the various types of text.
Logical, should the CMA type be shown in the title?
A color or a function that specifies the single
colour or the colour palette used to plot the different medication; by
default rainbow, but we recommend, whenever possible, a
colorblind-friendly palette such as viridis or colorblind_pal.
A string giving the name of the unspecified (generic) medication category.
The style of the event (line style, width, and start and end symbols).
Logical, should the actual event intervals be shown?
The colour used for missing event data.
Logical, should the CMA values be printed?
Logical, should the CMA values be represented graphically?
A number, the proportion of the total horizontal plot space to be allocated to the CMA plot.
Strings giving the colours of the various components of the CMA plot.
Logical, should the follow-up window be plotted?
The follow-up window's colour.
Logical, should the observation window be plotted?
Attributes of the observation window (colour, shading density, angle and opacity).
For some CMAs, the observation window might be adjusted, in which case should it be plotted and with that attributes?
Logical, should the daily dose be printed as text?
Numeric, if daily dose is printed, what text size to use?
If NA, don't print dose text with
outline, otherwise a color name/code for the outline.
Logical, print the daily dose centered on the segment or slightly below it?
Logical, should the daily dose be indicated through segment width?
Numeric, the segment width corresponding to the maximum daily dose (must be >= lwd.event but not too big either).
Logical, if TRUE,
the line width of the even is scaled relative to all medication classes (i.e.,
relative to the global minimum and maximum doses), otherwise it is scale
relative only to its medication class.
Logical, should the plot use grayscale only (i.e., the
gray.colors function)?
Numeric, the minimum size of the plotting surface in characters; horizontally (min.plot.size.in.characters.horiz) referes to the the whole duration of the events to plot; vertically (min.plot.size.in.characters.vert) referes to a single event.
Numeric, the maximum patients to attempt to plot.
Please note that this function plots objects inheriting from CMA0 but
not objects of type CMA0 itself (these are plotted by
plot.CMA0).
The x-axis represents time (either in days since the earliest date or as actual dates), with consecutive events represented as ascending on the y-axis.
Each event is represented as a segment with style lty.event and line
width lwd.event starting with a pch.start.event and ending with
a pch.end.event character, coloured with a unique color as given by
col.cats, extending from its start date until its end date.
Superimposed on these are shown the event intervals and gap days as estimated
by the particular CMA method, more precisely plotting the start and end of
the available events as solid filled-in rectangles, and the event gaps as
shaded rectangles.
The follow-up and the observation windows are plotted as an empty rectangle and as shaded rectangle, respectively (for some CMAs the observation window might be adjusted in which case the adjustment may also be plotted using a different shading).
The CMA estimates can be visually represented as well in the left side of the figure using bars (sometimes the estimates can go above 100%, in which case the maximum possible bar filling is adjusted to reflect this).
When several patients are displayed on the same plot, they are organized
vertically, and alternating bands (white and gray) help distinguish
consecutive patients.
Implicitely, all patients contained in the cma object will be plotted,
but the patients.to.plot parameter allows the selection of a subset of
patients.
Finally, the y-axis shows the patient ID and possibly the CMA estimate as well.
# NOT RUN {
cma1 <- CMA1(data=med.events,
ID.colname="PATIENT_ID",
event.date.colname="DATE",
event.duration.colname="DURATION",
followup.window.start=30,
observation.window.start=30,
observation.window.duration=365,
date.format="%m/%d/%Y"
);
plot(cma1, patients.to.plot=c("1","2"));
# }
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