Visualizations of different modules are combined by subject. The plots are aligned in the time axis (if requested). If the plots should be aligned:
the same time limits are set for all plots
the time axis is transformed if any of the plot was created with a time transformation
the time axis is expanded for all plots
if any of the plot was created with a time axis expanded.
The expansion object for
the combined plot is created
from the max of each expansion element across modules.
If some plots are missing for a specific subject,
an empty plot is created, containing information
as a text based on the label with which the plot was created.
subjectProfileCombine(
listPlots,
timeLim = NULL,
timeAlign = "all",
timeAlignPerSubject = "none",
subjectVar = "USUBJID",
maxNLines = NULL,
refLines = NULL,
refLinesData = NULL,
refLinesTimeVar = NULL,
refLinesLabelVar = NULL,
shiny = FALSE,
verbose = FALSE,
nCores = 1,
reportPerSubject = FALSE
)a nested list of ggplot object,
containing the combined
profile plots across modules for each subject/page.
Each plot object contains in the associated attribute:
metaData containing: nLines: an estimation
of the number of 'lines' each plot occupies
(e.g. to set height of the exported figure).
listPlots per subject as created inside the
subjectProfileCombine function.
time limits, as returned by the
getTimeLimSubjectProfilePlots function.
Character vector with time alignment across modules/subjects, either:
'all' (by default): all plots have the same time limits
'none': each of the plot (module*subject) has its own time limits
character vector with names of the modules which
should have the same time limits
(should correspond to the names of listPlots)
Character vector, specifying if the plots should be aligned (or not) across subjects
'none' (by default): all modules to align have the same time limit across subjects
'all': all modules to align have different time limits per subject
character vector with subset of the modules to align per subject
(should correspond to the names of listPlots)
Only the modules already specified in timeAlign
can be aligned by subject.
String, variable of data with subject ID
Maximum number of lines for a combined plot,
to fit in the page height.
When the different visualizations
are combined for each subject, they will be allocated
to different pages if the number of lines of the combined visualization
is higher than this number.
(optional) nested list with details for reference line(s). Each sublist contains:
(required) 'label': string with label for the reference line
(required) 'time': unique time (x) coordinate for the reference line
(optional) 'color': color for the reference line, 'black' by default
(optional) 'linetype': linetype for the reference line, 'dotted' by default
data.frame with data from which the reference line(s) should be extracted
string, variable of refLinesData with time for reference line(s)
string, variable of refLinesData with label for reference line(s)
logical, set to TRUE (FALSE by default)
if the report is generated from a Shiny application.
Messages during report creation will be included in the Shiny interface,
and it will be mentioned at the end of the report.
In this case, the shiny package should be available.
logical, if TRUE print messages during execution
Integer containing the number of cores used for the computation
(1 by default). If more than 1, computation is parallelized, in this case
the package parallel is required.
Logical, if TRUE (FALSE by default) export a subject profile report by subject.
Laure Cougnaud