Dear all,
I realise that xpose4 is perceived as getting a bit old, but as far as I can
tell it is still very widely used in the community, and auto-generated R-code
from PsN still uses xpose4. My own hesitation has always been in the perceived
lack of options to customise the output, but it has so many handy features 😊.
Currently I'm running VPCs with multi-level stratification implemented using
the STRT variable in NONMEM code, and my resulting VPCs have 4 graphs. However,
the headings of these graphs are the pretty ugly "STRT==0.5", "STRT==101" etc.
Is there a way to change this to a nice factor with customisable layout? And
while we're at it: is there a way to access/extract the individual graphs so
these can be formatted and/or printed separately?
Thanks very much in advance!
Kind regards,
Rik
xpose4::xpose.VPC(pc.info='vpc_results.csv',
vpctab='vpctab008',#xlim=c(0,42),
PI='lines',type='n',PI.identify.outliers=FALSE,#by='STRT',
PI.x.median=TRUE,
PI.ci.area.smooth=TRUE,
PI.rug=FALSE,
PI.ci.up.arcol="dodgerblue",
PI.ci.down.arcol="dodgerblue",
PI.real.med.col="brown",
PI.real.up.col="brown",
PI.real.down.col="brown",col="brown",
main="VPC final model",ylb="Drug X (ng/mL)",xlb="Time
(h)",ylim=c(0.01,120),logy=TRUE,
scales = list(x = list(at = seq(0,36,3))))
Rik Schoemaker, PhD
Occams Coöperatie U.A.
Malandolaan 10
1187 HE Amstelveen
The Netherlands
http://www.occams.com
+31 20 441 6410
[email protected]<mailto:[email protected]>
[cid:[email protected]]
Updating xpose4 stratification headers in VPCs
Hi Rik,
Indeed, you can make it prettier, more informative and more ggplot-like (but it
is still a lattice plot).
You can change the xposeVPC object (vpcPlot, in my example), e.g. setting size
of strip labels, y-label, etc, by updating the plot list.
vpcPlot@plotList[[1]] <- update(vpcPlot@plotList[[1]],[here you enter
arguments, like ylab=list(“Your y-label",cex=2)])
Then, you can select what panels you want to include, and give them the
appropriate strip-label text:
PrettierPlot <- c(“Dose A"=vpcPlot@plotList[[1]],
“Dose B"=vpcPlot@plotList[[3]],
“Dose C"=vpcPlot@plotList[[5]],layout = c(3,1))
That last step one has to be careful, as it is a bit error prone: you manually
set the labels and if you get it wrong it will be mislabelled.
Best regards
Jakob
Jakob Ribbing, Ph.D.
Senior Consultant, Pharmetheus AB
Cell/Mobile: +46 (0)70 514 33 77
[email protected]
www.pharmetheus.com
Phone, Office: +46 (0)18 513 328
Uppsala Science Park, Dag Hammarskjölds väg 36B
SE-752 37 Uppsala, Sweden
This communication is confidential and is only intended for the use of the
individual or entity to which it is directed. It may contain information that
is privileged and exempt from disclosure under applicable law. If you are not
the intended recipient please notify us immediately. Please do not copy it or
disclose its contents to any other person.
Quoted reply history
> On 24 Sep 2020, at 08:34, Rik Schoemaker <[email protected]> wrote:
>
> Dear all,
>
> I realise that xpose4 is perceived as getting a bit old, but as far as I can
> tell it is still very widely used in the community, and auto-generated R-code
> from PsN still uses xpose4. My own hesitation has always been in the
> perceived lack of options to customise the output, but it has so many handy
> features 😊. Currently I'm running VPCs with multi-level stratification
> implemented using the STRT variable in NONMEM code, and my resulting VPCs
> have 4 graphs. However, the headings of these graphs are the pretty ugly
> "STRT==0.5", "STRT==101" etc. Is there a way to change this to a nice factor
> with customisable layout? And while we're at it: is there a way to
> access/extract the individual graphs so these can be formatted and/or printed
> separately?
>
> Thanks very much in advance!
>
> Kind regards,
>
> Rik
>
>
> xpose4::xpose.VPC(pc.info http://pc.info/='vpc_results.csv',
> vpctab='vpctab008',#xlim=c(0,42),
>
> PI='lines',type='n',PI.identify.outliers=FALSE,#by='STRT',
> PI.x.median=TRUE,
> PI.ci.area.smooth=TRUE,
> PI.rug=FALSE,
> PI.ci.up.arcol="dodgerblue",
> PI.ci.down.arcol="dodgerblue",
> PI.real.med.col="brown",
> PI.real.up.col="brown",
> PI.real.down.col="brown",col="brown",
> main="VPC final model",ylb="Drug X
> (ng/mL)",xlb="Time (h)",ylim=c(0.01,120),logy=TRUE,
> scales = list(x = list(at = seq(0,36,3))))
>
>
> Rik Schoemaker, PhD
> Occams Coöperatie U.A.
> Malandolaan 10
> 1187 HE Amstelveen
> The Netherlands
> www.occams.com http://www.occams.com/
> +31 20 441 6410
> [email protected] <mailto:[email protected]>
>
> <image001.png>
Dear Rik,
You can alter the sub headings with 'main.sub=c("Plot 1 name","Plot 2
name", ...)'
It is also worth knowing that you can select plots for specific strata this
way:
VPCS <- xpose4::xpose.VPC(pc.info='vpc_results.csv', vpctab='vpctab008')
listVPCS <- VPCS@plotList # List of VPC plots for all strata
VPC1 <- listVPCS[[1]] # VPC for first strata
VPC2 <- listVPCS[[2]] # VPC for second strata
Kind regards,
Martin Bergstrand, Ph.D.
Principal Consultant
Pharmetheus AB
+46(0)709 994 396
[email protected]
www.pharmetheus.com
*This communication is confidential and is only intended for the use of the
individual or entity to which it is directed. It may contain information
that is privileged and exempt from disclosure under applicable law. If you
are not the intended recipient please notify us immediately. Please do not
copy it or disclose its contents to any other person.*
Quoted reply history
On Thu, Sep 24, 2020 at 8:43 AM Rik Schoemaker <[email protected]>
wrote:
> Dear all,
>
>
>
> I realise that xpose4 is perceived as getting a bit old, but as far as I
> can tell it is still very widely used in the community, and auto-generated
> R-code from PsN still uses xpose4. My own hesitation has always been in the
> perceived lack of options to customise the output, but it has so many handy
> features 😊. Currently I'm running VPCs with multi-level stratification
> implemented using the STRT variable in NONMEM code, and my resulting VPCs
> have 4 graphs. However, the headings of these graphs are the pretty ugly
> "STRT==0.5", "STRT==101" etc. Is there a way to change this to a nice
> factor with customisable layout? And while we're at it: is there a way to
> access/extract the individual graphs so these can be formatted and/or
> printed separately?
>
>
>
> Thanks very much in advance!
>
>
>
> Kind regards,
>
>
>
> Rik
>
>
>
>
>
> xpose4::xpose.VPC(pc.info='vpc_results.csv',
>
> vpctab='vpctab008',#xlim=c(0,42),
>
>
> PI='lines',type='n',PI.identify.outliers=FALSE,#by='STRT',
>
> PI.x.median=TRUE,
>
> PI.ci.area.smooth=TRUE,
>
> PI.rug=FALSE,
>
> PI.ci.up.arcol="dodgerblue",
>
> PI.ci.down.arcol="dodgerblue",
>
> PI.real.med.col="brown",
>
> PI.real.up.col="brown",
>
> PI.real.down.col="brown",col="brown",
>
> main="VPC final model",ylb="Drug X
> (ng/mL)",xlb="Time (h)",ylim=c(0.01,120),logy=TRUE,
>
> scales = list(x = list(at = seq(0,36,3))))
>
>
>
>
>
> *Rik Schoemaker, PhD*
>
> *Occams *Coöperatie U.A.
> Malandolaan 10
> 1187 HE Amstelveen
> The Netherlands
>
> www.occams.com
>
> +31 20 441 6410
> [email protected]
>
>
>
>
>
--
Martin Bergstrand, Ph.D.
Principal Consultant
Pharmetheus AB
+46(0)709 994 396
[email protected]
www.pharmetheus.com
+46(0)18 513 328
U-A Science Park, Dag Hammarskjölds v. 36b
752 37 Uppsala, Sweden
*This communication is confidential and is only intended for the use of the
individual or entity to which it is directed. It may contain information
that is privileged and exempt from disclosure under applicable law. If you
are not the intended recipient please notify us immediately. Please do not
copy it or disclose its contents to any other person.*
Hello Rik,
xpose4 is based on lattice package, most of lattice arguments/options can
be passed to xpose4. To change the label of each stratum you can use this
option;
*strip=strip.custom(factor.levels=myStrataLabel) *; myStrataLabel is
character vectors containing label for each of your stratum
to access or change the order of each stratification, you can use this
option
*index.cond = list(c(1,2,3,4...n))*, # Set order of sub-plots
Mahmoud
Quoted reply history
On Thu, Sep 24, 2020 at 8:50 AM Rik Schoemaker <[email protected]>
wrote:
> Dear all,
>
>
>
> I realise that xpose4 is perceived as getting a bit old, but as far as I
> can tell it is still very widely used in the community, and auto-generated
> R-code from PsN still uses xpose4. My own hesitation has always been in the
> perceived lack of options to customise the output, but it has so many handy
> features 😊. Currently I'm running VPCs with multi-level stratification
> implemented using the STRT variable in NONMEM code, and my resulting VPCs
> have 4 graphs. However, the headings of these graphs are the pretty ugly
> "STRT==0.5", "STRT==101" etc. Is there a way to change this to a nice
> factor with customisable layout? And while we're at it: is there a way to
> access/extract the individual graphs so these can be formatted and/or
> printed separately?
>
>
>
> Thanks very much in advance!
>
>
>
> Kind regards,
>
>
>
> Rik
>
>
>
>
>
> xpose4::xpose.VPC(pc.info='vpc_results.csv',
>
> vpctab='vpctab008',#xlim=c(0,42),
>
>
> PI='lines',type='n',PI.identify.outliers=FALSE,#by='STRT',
>
> PI.x.median=TRUE,
>
> PI.ci.area.smooth=TRUE,
>
> PI.rug=FALSE,
>
> PI.ci.up.arcol="dodgerblue",
>
> PI.ci.down.arcol="dodgerblue",
>
> PI.real.med.col="brown",
>
> PI.real.up.col="brown",
>
> PI.real.down.col="brown",col="brown",
>
> main="VPC final model",ylb="Drug X
> (ng/mL)",xlb="Time (h)",ylim=c(0.01,120),logy=TRUE,
>
> scales = list(x = list(at = seq(0,36,3))))
>
>
>
>
>
> *Rik Schoemaker, PhD*
>
> *Occams *Coöperatie U.A.
> Malandolaan 10
> 1187 HE Amstelveen
> The Netherlands
>
> www.occams.com
>
> +31 20 441 6410
> [email protected]
>
>
>
>
>
--
*Mahmoud Tareq AbdelwahabPhD StudentPharmacometrics Research GroupDivision
of Clinical PharmacologyDepartment of MedicineUniversity of Cape TownK45
Old Main BuildingGroote Schuur HospitalObservatory, Cape Town 7925, South
Africa.*
*Tel: +27 21 650 4861Email: [email protected] <[email protected]>*