plot.CMA0 {AdhereR}R Documentation

Plot CMA0 objects.

Description

Plots the events (prescribing or dispensing) data encapsulated in a basic CMA0 object.

Usage

## S3 method for class 'CMA0'
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,
  xlab = c(dates = "Date", days = "Days"),
  ylab = c(withoutCMA = "patient", withCMA = "patient (& CMA)"),
  title = c(aligned = "Event patterns (all patients aligned)", notaligned =
    "Event patterns"),
  col.cats = rainbow,
  unspecified.category.label = "drug",
  medication.groups.to.plot = NULL,
  medication.groups.separator.show = TRUE,
  medication.groups.separator.lty = "solid",
  medication.groups.separator.lwd = 2,
  medication.groups.separator.color = "blue",
  medication.groups.allother.label = "*",
  lty.event = "solid",
  lwd.event = 2,
  pch.start.event = 15,
  pch.end.event = 16,
  plot.events.vertically.displaced = TRUE,
  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,
  col.continuation = "black",
  lty.continuation = "dotted",
  lwd.continuation = 1,
  col.na = "lightgray",
  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,
  alternating.bands.cols = c("white", "gray95"),
  force.draw.text = FALSE,
  bw.plot = FALSE,
  min.plot.size.in.characters.horiz = 0,
  min.plot.size.in.characters.vert = 0,
  suppress.warnings = FALSE,
  max.patients.to.plot = 100,
  export.formats = NULL,
  export.formats.fileprefix = "AdhereR-plot",
  export.formats.height = NA,
  export.formats.width = NA,
  export.formats.save.svg.placeholder = TRUE,
  export.formats.svg.placeholder.type = c("jpg", "png", "webp")[2],
  export.formats.svg.placeholder.embed = FALSE,
  export.formats.html.template = NULL,
  export.formats.html.javascript = NULL,
  export.formats.html.css = NULL,
  export.formats.directory = NA,
  generate.R.plot = TRUE
)

Arguments

x

A CMA0 or derived object, representing the CMA to plot

...

other possible parameters

patients.to.plot

A vector of strings containing the list of patient IDs to plot (a subset of those in the cma object), or NULL for all

duration

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.

align.all.patients

Logical, should all patients be aligned (i.e., the actual dates are discarded and all plots are relative to the earliest date)?

align.first.event.at.zero

Logical, should the first event be placed at the origin of the time axis (at 0)?

show.period

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".

period.in.days

The number of days at which the regular grid is drawn (or 0 for no grid).

show.legend

Logical, should the legend be drawn?

legend.x

The position of the legend on the x axis; can be "left", "right" (default), or a numeric value.

legend.y

The position of the legend on the y axis; can be "bottom" (default), "top", or a numeric value.

legend.bkg.opacity

A number between 0.0 and 1.0 specifying the opacity of the legend background.

cex, cex.axis, cex.lab, legend.cex, legend.cex.title

numeric values specifying the cex of the various types of text.

xlab

Named vector of x-axis labels to show for the two types of periods ("days" and "dates"), or a single value for both, or NULL for nothing.

ylab

Named vector of y-axis labels to show without and with CMA estimates, or a single value for both, or NULL for nonthing.

title

Named vector of titles to show for and without alignment, or a single value for both, or NULL for nonthing.

col.cats

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.

unspecified.category.label

A string giving the name of the unspecified (generic) medication category.

medication.groups.to.plot

the names of the medication groups to plot or NULL (the default) for all.

medication.groups.separator.show

a boolean, if TRUE (the default) visually mark the medication groups the belong to the same patient, using horizontal lines and alternating vertical lines.

medication.groups.separator.lty, medication.groups.separator.lwd, medication.groups.separator.color

graphical parameters (line type, line width and colour describing the visual marking og medication groups as beloning to the same patient.

medication.groups.allother.label

a string giving the label to use for the implicit __ALL_OTHERS__ medication group (defaults to "*").

lty.event, lwd.event, pch.start.event, pch.end.event

The style of the event (line style, width, and start and end symbols).

plot.events.vertically.displaced

Should consecutive events be plotted on separate rows (i.e., separated vertically, the default) or on the same row?

print.dose

Logical, should the daily dose be printed as text?

cex.dose

Numeric, if daily dose is printed, what text size to use?

print.dose.outline.col

If NA, don't print dose text with outline, otherwise a color name/code for the outline.

print.dose.centered

Logical, print the daily dose centered on the segment or slightly below it?

plot.dose

Logical, should the daily dose be indicated through segment width?

lwd.event.max.dose

Numeric, the segment width corresponding to the maximum daily dose (must be >= lwd.event but not too big either).

plot.dose.lwd.across.medication.classes

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.

col.continuation, lty.continuation, lwd.continuation

The style of the "continuation" lines connecting consecutive events (colour, line style and width).

col.na

The colour used for missing event data.

highlight.followup.window

Logical, should the follow-up window be plotted?

followup.window.col

The follow-up window's colour.

highlight.observation.window

Logical, should the observation window be plotted?

observation.window.col, observation.window.density, observation.window.angle, observation.window.opacity

Attributes of the observation window (colour, shading density, angle and opacity).

alternating.bands.cols

The colors of the alternating vertical bands distinguishing the patients; can be NULL = don't draw the bandes; or a vector of colors.

force.draw.text

Logical, if TRUE, always draw text even if too big or too small

bw.plot

Logical, should the plot use grayscale only (i.e., the gray.colors function)?

min.plot.size.in.characters.horiz, min.plot.size.in.characters.vert

Numeric, the minimum size of the plotting surface in characters; horizontally (min.plot.size.in.characters.horiz) refers to the the whole duration of the events to plot; vertically (min.plot.size.in.characters.vert) refers to a single event. If the plotting is too small, possible solutions might be: if within RStudio, try to enlarge the "Plots" panel, or (also valid outside RStudio but not if using RStudio server start a new plotting device (e.g., using X11(), quartz() or windows(), depending on OS) or (works always) save to an image (e.g., jpeg(...); ...; dev.off()) and display it in a viewer.

suppress.warnings

Logical: show or hide the warnings?

max.patients.to.plot

Numeric, the maximum patients to attempt to plot.

export.formats

a string giving the formats to export the figure to (by default NULL, meaning no exporting); can be any combination of "svg" (just an SVG file), "html" (SVG + HTML + CSS + JavaScript, all embedded within one HTML document), "jpg", "png", "webp", "ps" or "pdf".

export.formats.fileprefix

a string giving the file name prefix for the exported formats (defaults to "AdhereR-plot").

export.formats.height, export.formats.width

numbers giving the desired dimensions (in pixels) for the exported figure (defaults to sane values if NA).

export.formats.save.svg.placeholder

a logical, if TRUE, save an image placeholder of type given by export.formats.svg.placeholder.type for the SVG image.

export.formats.svg.placeholder.type

a string, giving the type of placeholder for the SVG image to save; can be "jpg", "png" (the default) or "webp".

export.formats.svg.placeholder.embed

a logical, if TRUE, embed the placeholder image in the HTML document (if any) using base64 encoding, otherwise (the default) leave it as an external image file (works only when an HTML document is exported and only for JPEG or PNG images.

export.formats.html.template, export.formats.html.javascript, export.formats.html.css

character strings or NULL (the default) giving the path to the HTML, JavaScript and CSS templates, respectively, to be used when generating the HTML+CSS semi-interactive plots; when NULL, the default ones included with the package will be used. If you decide to define new templates please use the default ones for inspiration and note that future version are not guaranteed to be backwards compatible!

export.formats.directory

a string; if exporting, which directory to export to; if NA (the default), creates the files in a temporary directory.

generate.R.plot

a logical, if TRUE (the default), generate the standard (base R) plot for plotting within R.

Details

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. Consecutive events are thus represented on consecutive levels of the y-axis and are connected by a "continuation" line with col.continuation colour, lty.continuation style and lwd.continuation width; these continuation lines are purely visual guides helping to perceive the sequence of events, and carry no information about the availability of medication in this interval.

When several patients are displayed on the same plot, they are organized vertically, and alternating bands (white and gray) help distinguish consecutive patients. Implicitly, all patients contained in the cma object will be plotted, but the patients.to.plot parameter allows the selection of a subset of patients.

Examples

cma0 <- CMA0(data=med.events,
             ID.colname="PATIENT_ID",
             event.date.colname="DATE",
             event.duration.colname="DURATION",
             event.daily.dose.colname="PERDAY",
             medication.class.colname="CATEGORY",
             followup.window.start=0,
             followup.window.start.unit="days",
             followup.window.duration=2*365,
             followup.window.duration.unit="days",
             observation.window.start=30,
             observation.window.start.unit="days",
             observation.window.duration=365,
             observation.window.duration.unit="days",
             date.format="%m/%d/%Y",
             summary="Base CMA");
plot(cma0, patients.to.plot=c("1","2"));

[Package AdhereR version 0.7.0 Index]