Section Breaks appear to not be functioning for calls to subjectProfileLinePlot and subjectProfileTextPlot

[renelaurer]

I am having difficultly adding section breaks and section break titles between the patientProfilesVis R package sections. For example I am running these calls to the patientProfilesVis package:

egPlot2 <- subjectProfileTextPlot(
data = dataEG,
paramValueVar = c("EGTEST", "EGORRES", "EGORRESU", "EGDTC"),
paramGroupVar = c("EGDTC" ),
title = " Electrocardiogram ECG (Start - End)",
labelVars = labelVars,
paging = TRUE,
table = TRUE,
subjectVar = "SUBJID"
)
patientProfilesPlots <- c(patientProfilesPlots, list(EH = egPlot2))

moPlots <- subjectProfileTextPlot(
data = dataMO,
paramValueVar = c("MOCAT", "MOORRES", "MODTC"),
paramGroupVar = c("MODTC" ),
title = " Clinical Assessment of Radiograph Imaging (Start - End)",
labelVars = labelVars,
paging = TRUE,
table = TRUE,
subjectVar = "SUBJID"
)
patientProfilesPlots <- c(patientProfilesPlots, list(MO = moPlots))

prPlots <- subjectProfileTextPlot(
data = dataADPR,
paramValueVar = c("PRDECOD", "PRTERM", "PRSTDTC", "PRENDTC"),
title = "Concomitant Non Drug Procedures (Start - End)",
labelVars = labelVars,
paging = TRUE,
table = TRUE,
subjectVar = "SUBJID"
)
patientProfilesPlots <- c(patientProfilesPlots, list(PR = prPlots))

The patientProvilesVis calls above generate the PDF file output

Notice that the output produced has no section breaks and no section break titles are displayed between the 3 calls to subjectProfileTextPlot().

I did create values for the sectionTitles though. If you run the code in R Studio, then click on the template tab (in R Studio) for subjectProfile.Rnw, here we can see that the section breaks are defined and are associated with the listPlots object.
Simply run this R code in R Studio to view the section break values:

sectionTitles <- sapply( seq_along(listPlotsPerSubjectList), function(i) {

•    attr( listPlotsPerSubjectList[[i]], "metaData")$label   })
  

sectionTitles[10:12]
[1] " Electrocardiogram ECG (Start - End)" " Clinical Assessment of Radiograph Imaging (Start - End)" "Concomitant Non Drug Procedures (Start - End)"

My reference above to elements 10 to 12 is just to illustrate a section of my total PDF output and a section of the total R code. I am including 3 sections of the code and 3 associated sections of the PDF file output.

So above you can see that I have taken steps to associate the section breaks and the section break titles with the listPlotsperSubjectList object. And yet the PatientProfileVis package seems to not display my section breaks and section titles in my PDF output.

Please note that the original R package for PatientProfileVis defines the sectionTitles in this way:
sectionTitles <- unlist(lapply(names(listPlotsPerSubjectList), function(subject)
c(subject, rep("", length(listPlotsPerSubjectList[[subject]])-1)))
)

I have found that this does not work though as it also does not properly associate my sectionTitles values to the PDF output produced.

I would really like to get section breaks and section titles to work. I am investing a lot of hours into getting this to work.
If anyone has examples of the patientProfilesVis R package working probably with regards to the sectionTitles processing then please send those hints and suggestions to me. This is a priority for me.

[lcougnaud]

Thanks for your interest in the package!

Notice that the output produced has no section breaks and no section break titles are displayed between the 3 calls to subjectProfileTextPlot().

To specify a linebreak in the plot title, could you specify '\n' in the title, as the following?

dmPlots <- subjectProfileTextPlot(
  data = dataSDTM$DM,
  paramValueVar = c("SEX|AGE", "RACE|COUNTRY", "ARM"),
  labelVars = labelVarsSDTM,
  title = "Subject information\nDemographic variables"
)

I did create values for the sectionTitles though. If you run the code in R Studio, then click on the template tab (in R Studio) for subjectProfile.Rnw, here we can see that the section breaks are defined and are associated with the listPlots object. Simply run this R code in R Studio to view the section break values:

sectionTitles <- sapply( seq_along(listPlotsPerSubjectList), function(i)  {
     attr( listPlotsPerSubjectList[[i]], "metaData")$label   })

sectionTitles[10:12]
[1] " Electrocardiogram ECG (Start - End)" " Clinical Assessment of Radiograph Imaging (Start - End)" "Concomitant Non Drug Procedures (Start - End)"

The sectionTitles object should contain the titles for each subject and plot modules, not only for each plot modules. Could you try the solution mention above? The subjectProfile.Rnw template is not meant to be updated/used directly by the user, but used internally via the createSubjectProfileReport function.

I have found that this does not work though as it also does not properly associate my sectionTitles values to the PDF output produced.

Could you include an example which shows what doesn't work in the section titles?

[renelaurer]

I have considered your points above and I have tried a few things to see if I can reach my goal of adding in " Section Breaks ". Unfortunately , following your suggestions above I have not been able to add in sectionTitles or section breaks. Here I am using section break to mean the numbers and titles that appear between output sections.

Perhaps I was not explaining that well enough above from my original message on this thread.
From my original issue I will try to explain what I mean more completely here.
I encounter this output currently:

Notice above how the 3 sections above Electrocardiogram ECG , Clinical Assessment of Radiograph Image, and lastly Concomitant Non Drug Procedures all appear next to each other with no section break and they are dangerously close to each other when the are printed to my PDF output file.

What I am trying to figure out is how to achieve something similar to this:

Notice above that the " section breaks " can separate the 3 output sections. They add numbering between the sections and they can hopefully create a page break as well. I am wondering if the output can have sections breaks to make the PDF output easier to read. Each section (or subsection) can be generated by something like:
cat("\subsection{", sectionTitles[i], "} \n", sep = "" )
or perhaps even this:
cat("\section{", sectionTitles[i], "} \n", sep = "" )

I have populated sectionTitles at all levels of my patientProfilesPlots object. I pass in patientProfilesPlots to the createSubjectProfileReport. I have populated the labels at the top level and the sub levels as well. My command to generate the final PDF file is:

pathsPatientProfiles <- createSubjectProfileReport(
listPlots = patientProfilesPlots,
reportPerSubject = TRUE,
verbose = TRUE,
outputFile = paste0('PDR_', study, '.pdf') ,
timeAlign = "none",
timeAlignPerSubject = "none",
exportBatchSize = 5,
subjectSortData = dataDM,
subjectSortVar = "SUBJID",
subjectVar = "SUBJID" ,
maxNLine = 56,
subjectSortDecreasing = FALSE
)

Notice above that I pass in patientProfilesPlots. And here are the labels which I have defined for this object:

attr(patientProfilesPlots$DM, "metaData")$label
[1] "Demographics"
attr(patientProfilesPlots$EX, "metaData")$label
[1] "Treatment Exposure"
attr(patientProfilesPlots$DM$"10131001", "metaData")$label
[1] "Demographics"
attr(patientProfilesPlots$EX$"11091048", "metaData")$label
[1] "Treatment Exposure"

As we can see above, I have defined levels at both the top data domain level ( Adverse Events, Demographics, Treatment Exposure, and so on) as well as at the Subject ID level as well. With the Subjects appearing below the data domain level.

At every level of the patientProfilesPlots object I have defined labels. I have done this in hopes that those labels may appear later as a new section or a new sub-section in the final PDF output. But so far, this has been very difficult to get working.

Would you have any examples of sectionTitles working or the addition of section breaks between output sections ?
I am trying to get a good separation between PDF output sections. Does this make sense ?

Thanks,
-Rene

[lcougnaud]

Hi Rene,

Sorry for the very late reply.
This will require a few updates to the package:

• update how the different 'modules' (in your case ECG, radiography and concomitant medications) visualizations are combined (for each subject) & included in the report
• update the internal template Rnw file available in the package.
  By default, the different 'modules' are combined such as the different visualizations are combined to fit within one single a4 page.

As this will require quite some changes in the package, could you let me know if this issue is still relevant for you?