Visualize time interval in subject profiles, so event with a start and end time.
subjectProfileIntervalPlot(
data,
paramVar,
paramVarSep = " - ",
paramLab = getLabelVar(paramVar, labelVars = labelVars),
paramGroupVar = NULL,
timeStartVar,
timeStartLab = getLabelVar(timeStartVar, labelVars = labelVars),
timeEndVar,
timeEndLab = getLabelVar(timeEndVar, labelVars = labelVars),
timeLab = toString(c(timeStartLab, timeEndLab)),
subjectVar = "USUBJID",
subjectSubset = NULL,
subjectSample = NULL,
seed = 123,
subsetData = NULL,
subsetVar = NULL,
subsetValue = NULL,
timeImpType = c("minimal", "data-based", "none"),
timeLim = NULL,
timeLimData = NULL,
timeLimStartVar = NULL,
timeLimStartLab = getLabelVar(timeLimStartVar, labelVars = labelVars),
timeLimEndVar = NULL,
timeLimEndLab = getLabelVar(timeLimEndVar, labelVars = labelVars),
timeTrans = NULL,
timeExpand = NULL,
timeAlign = TRUE,
xLab = timeLab,
yLab = "",
colorVar = NULL,
colorLab = getLabelVar(colorVar, labelVars = labelVars),
colorPalette = NULL,
alpha = 1,
timeStartShapeVar = NULL,
timeEndShapeVar = NULL,
shapePalette = NULL,
shapeLab = toString(unique(getLabelVar(c(timeStartShapeVar, timeEndShapeVar), labelVars
= labelVars))),
shapeSize = rel(3),
title = toString(getLabelVar(paramVar, labelVars = labelVars, label = paramLab)),
label = title,
caption,
labelVars = NULL,
formatReport = subjectProfileReportFormat(),
paging = TRUE
)list of (across subjects) of list (across pages)
of ggplot2 objects,
also of class subjectProfileIntervalPlot.
with additional 'metaData' attributes containing
'label', 'timeLim' timeTrans and timeExpand (if specified).
Data.frame with data.
Character vector with variable(s) of data
with parameters. Variable content is displayed in the y-axis.
string with character(s) used to concatenate multiple
paramVar, ' - ' by default.
Named character vector,
with label for the parameter variable(s) (paramVar).
This is used to set the default title.
(optional) Character vector with variable(s)
of data based on which the data will be grouped and sorted
(in the y-axis) in the plot.
String, variable of data
with start of time interval.
String, label for timeStartVar,
displayed in a message and in the plot caption.
String, variable of data
with end of time interval.
String, label for timeEndVar,
displayed in a message and in the plot caption.
String, label for timeVar.
This is used in the message
indicating missing values for timeVar,
and for the default label of the x-axis.
String, variable of data with subject ID
(optional) Character vector with subjects of interest
(available in subjectVar), NULL by default.
(optional) Integer of length 1 with number of random subject(s) that should be considered, e.g. to check the created patient profiles for a subset of the data. By default, all specified subjects are considered (set to NULL).
(optional) Integer of length 1 with seed used to select random subjects
if subjectSample is specified (123 by default).
(optional) Data.frame with extra dataset to filter on.
This dataset is filtered, and only records from data
with common subject IDs will be retained.
If not specified, data is used.
(optional) String with variable of subset data to filter on.
subsetValue should be specified too.
If not specified, all records from the subset data are retained.
(optional) Character vector with value(s) of interest to
retain in the filtered data.
These values should be available in subsetVar.
Missing values in the subject variable are not retained
in the filtered data.
String with imputation type: 'minimal' (default),
'data-based' or 'none', see section: 'Time interval representation'.
This imputation type is not used if a dataset used to impute time is
specified.
(optional) Vector of length 2 with time limits (x-axis).
If not specified, these are extracted from the minimum timeStartVar
and maximum timeEndVar per subject.
The time limits are stored as attributes of the plots,
used to align the plots in the final report.
Data.frame with data used to impute time
in case some time records are missing in data,
see section: 'Time interval representation'.
String, variable of timeLimData with
start of the time interval.
String, label for timeLimeStartVar,
displayed in a message and in the plot caption.
String, variable of timeLimData with
end of the time interval.
String, label for timeLimEndVar,
displayed in a message and in the plot caption.
transformation for the time variable,
(see trans parameter in scale_x_continuous, and
trans_new).
For example, produced by the getTimeTrans function.
Vector of range expansion constants for the time axis
(see expand parameter in scale_x_continuous).
Logical, if TRUE (by default)
the different plots are horizontally aligned.
If set to FALSE, each plot has its own time-limits.
If set to FALSE, this is not compatible with
the specification of timeLim.
String, label for the x-axis.
String, label for the y-axis.
String, variable of data with color,
used both for the point(s) and segment(s).
String, label for colorVar.
Named vector with color palette.
The variable should be named with the corresponding element
in colorVar.
Colors can also be defined for the entire session, by setting
options(patientProfilesVis.colors = X) with X either:
a vector with colors
a function returning a vector of colors for a specified number
of elements (viridis by default)
Numeric with transparency, 1 by default.
(optional) String, variable of data
used for the shape of the symbol displayed
at the start of the time interval.
If not specified, default shape palette is used,
see section 'Time interval representation'.
String, variable of data
used for the shape of the symbol
displayed at the end of the time interval.
If not specified, default shape palette is used,
see section 'Time interval representation'.
Named vector with (combined) shape palette for
timeStartShapeVartimeEndShapeVar.
String with label for timeStartShapeVartimeEndShapeVar
Size for symbols (only used if timeStartShapeVar/timeEndShapeVar is specified).
String with title, label of the parameter variable by default.
String, label for the visualization.
This label is stored as attributes of the output
from the subjectProfile[]Plot function.
This label is displayed in the final profile
report, in case no data is available for
for a specific patient, as: 'No [label] available.'
(optional) String with caption (NULL for no caption). By default the caption contains information on the imputation strategy for missing time.
Named character vector with variable labels (names are the variable code)
list with parameters used to specify the format of the report,
e.g. output of the subjectProfileReportFormat function
Logical, if TRUE (by default), automatic
paging is enabled, so patient profiles module too big to fit
in one page will span multiple pages.
Please note that the size of the graphic window
(or report page) may need
to be re-sized in order that the plot fits.
If FALSE, the entire plot is included in one single page.
In case the start or the end of the time interval contain missing values:
if a dataset (timeLimData), start (timeLimStartVar)
and end (timeLimEndVar) variables are specified:
for each subject:
the minimum and maximum time values across these specified time variables are extracted
missing start values are replaced by the minimum time
missing start values are replaced by the maximum time
if all values are missing for this subject, they are taken across subjects
otherwise, depending on the imputation type (timeImpType):
'minimal' (by default):
if the start and the end of the interval are missing: no imputation is done, only the label is displayed
if the start time is missing and the end time is not missing: start time is imputed with end time, and status is set to 'Missing start'
if the end time is missing and the start time is not missing: end time is imputed with start time, and status is set to 'Missing end'
'data-based' (default in version < 1.0.0): minimum/maximum values in the start/end time variables in the data are considered for the specific subject (if available). If there are missing for a specific subject, they are taken across subjects. If all time are missings, the range is set to 0 and Inf
'none': no imputation is done
The symbols displayed at the start and end of the interval are:
by default:
a filled square labelled 'Complete' if the time is not missing
a filled left-directed arrow in case of missing start time
a filled right-directed arrow in case of missing end time
if the variable(s) used for the shape of the start or end
of the interval are specified (via
timeStartShapeVar/timeEndShapeVar):
labels are based on these variables, and a standard shape palette is used
The time limits are the same across subjects, and set to:
timeLim if specified
maximum time range in timeLimStartVar and
timeLimEndVar in timeLimData
if specified
the maximum range on the data obtained after imputation of missing values
Laure Cougnaud
Other patient profiles plotting function:
subjectProfileEventPlot(),
subjectProfileLinePlot(),
subjectProfileTextPlot()