sbiotrellis
R2026bPlot data or simulation results in trellis plot
Syntax
Description
trellisplot = sbiotrellis(data,groupCol,xCol,yCol)data as defined by the group column
variable groupCol into its own subplot. The data defined by
column xCol is plotted against the data defined by column(s)
yCol.
trellisplot = sbiotrellis(data,fcnHandle,groupCol,xCol,yCol)data as defined by the group column
variable groupCol into its own subplot.
sbiotrellis creates the subplot by calling the function
handle, fcnHandle, with input arguments defined by the
data columns xCol and
yCol. The fcnHandle cannot be empty
and must be specified.
The fcnHandle must have the signature
fcnHandle(x,y), where x is a numeric
column vector, and y is a matrix with the same number of rows as
x.
For instance, if you want to create a trellis plot with a logarithmic
y-axis, use @semilogy as the function
handle, where semilogy is the function that plots
data with logarithmic scale for the y-axis.
trellisplot = sbiotrellis(simData,fcnHandle,xCol,yCol)simData into its own subplot.
sbiotrellis creates the subplot by calling the function
handle, fcnHandle with input arguments defined by the columns
xCol and yCol. The
fcnHandle can be empty ('' or
[]). If empty, a default time plot is created by plotting the
simulation time against the states specified in yCol.
The fcnHandle must have the signature
fcnHandle(simDataI,xCol,yCol), where
simDataI is a single SimData object, and
xCol and yCol are the corresponding input
arguments to sbiotrellis.
trellisplot = sbiotrellis(simDataArray1,simDataArray2,fcnHandle,y1,y2)simDataArray1 and
simDataArray2 into its own subplot.
sbiotrellis creates each subplot by calling the function
handle, fcnHandle, with one element from each
SimData array and the text arguments y1
and y2. Both SimData arrays must have the
same number of elements. The fcnHandle cannot be empty and must
be specified.
The fcnHandle must have the signature
fcnHandle(simData1I,simData2I,y1,y2), where
simData1I and simData2I are individual
SimData objects from simDataArray1 and
simDataArray2, and y1 and
y2 are the corresponding input arguments to
sbiotrellis.
Tip
Use the plot method of a sbiotrellis
object to overlay a SimData object or a
dataset on an existing sbiotrellis
plot. For example, plot(trellisplot,...) adds a plot to
the object trellisplot. The SimData or
dataset that is being plotted must have the same
number of elements or groups as the trellisplot object.
The plot method has the same input arguments as
sbiotrellis.
Examples
Load a sample dataset. The data contains measurements of drug concentration in the central and peripheral compartments for 30 subjects.
load('sd5_302RAgeSex.mat');Create a trellis plot of the Central concentrations for each subject.
t = sbiotrellis(data, 'ID', 'Time', 'CentralConc',... 'Marker', 'o','LineStyle','--','MarkerFaceColor','b'); % Resize the figure. t.hFig.Position(:) = [100 100 1200 800]; t.YLabel = "Concentration (milligram/liter)"; t.XLabel = "Time (hours)"; t.Title = "Drug Concentration Measurements";
Use the plot method of the sbiotrellis object to overlay the peripheral concentration data on the same plot.
plot(t,data,'ID','Time','PeripheralConc','Marker','d',... 'LineStyle',':','MarkerFaceColor','r');
Specify the function handle @semilogy to change the y-axis to log scale.
t2 = sbiotrellis(data,@semilogy,'ID','Time','CentralConc'); %Resize the figure t2.hFig.Position(:) = [100 100 1200 800];
plot(t2,data,@semilogy,'ID','Time','PeripheralConc');
Compare simulation results from two dosing regimens by plotting them side by side using sbiotrellis with SimData arrays.
Create a simple one-compartment model with first-order elimination.
model = sbiomodel("OneCptPK"); comp = addcompartment(model,"Central",1,CapacityUnits="liter"); addspecies(comp,"Drug",0,InitialAmountUnits="milligram"); addparameter(model,"ke",ValueUnits="1/hour"); rxn = addreaction(model,"Central.Drug -> null"); kl = addkineticlaw(rxn,"MassAction"); kl.ParameterVariableNames = "ke";
Set the simulation stop time to 24 hours and define two bolus doses at different amounts.
cs = getconfigset(model,"active"); cs.StopTime = 24; cs.TimeUnits = "hour"; doseHigh = sbiodose("HighDose",Amount=100,AmountUnits="milligram",TargetName="Central.Drug"); doseLow = sbiodose("LowDose",Amount=25,AmountUnits="milligram",TargetName="Central.Drug");
Simulate four subjects with different elimination rates under the high-dose regimen.
keValues = [0.05 0.1 0.15 0.2]; for i = numel(keValues):-1:1 model.Parameters(1).Value = keValues(i); sdHigh(i,1) = sbiosimulate(model,doseHigh); end
Use sbiotrellis with a single SimData array and a function handle to create a trellis plot with filled area curves. The function handle receives one SimData element per panel along with the column name arguments xCol and yCol.
trellisplot = sbiotrellis(sdHigh,@areaPlot,"Time","Drug"); trellisplot.Title = "High Dose (100 mg) - Area Plot"; trellisplot.XLabel = "Time (hours)"; trellisplot.YLabel = "Drug Concentration (mg/L)";
Now simulate the same four subjects under the low-dose regimen and compare both sets of results using sbiotrellis with two SimData arrays.
for i = numel(keValues):-1:1 model.Parameters(1).Value = keValues(i); sdLow(i,1) = sbiosimulate(model,doseLow); end
Use sbiotrellis with two SimData arrays and a custom function handle to overlay results from both doses in each panel. The function handle receives one element from each array per panel and plots them together.
trellisplot2 = sbiotrellis(sdHigh,sdLow,@compareDoses,"Drug","Drug"); trellisplot2.Title = "High Dose (100 mg) vs Low Dose (25 mg)"; trellisplot2.XLabel = "Time (hours)"; trellisplot2.YLabel = "Drug Concentration (mg/L)"; trellisplot2.updateLegend(["High Dose","Low Dose"]);
Each panel corresponds to one subject. The blue solid line shows the high-dose response and the red dashed line shows the low-dose response.
The function handle areaPlot is defined as a local function. It receives a single SimData object and the column name arguments xCol and yCol. It uses selectbyname to extract the data for yCol, displays it as a filled area curve, and uses xCol to label the x-axis.
The function handle compareDoses is defined as a local function. It receives one SimData object from each array and the text arguments y1 and y2, which in this case are both "Drug" — the name of the species to extract from each SimData object. It uses selectbyname to extract the time and data vectors, then overlays both results on the same axes.
function areaPlot(sdI,xCol,yCol) [t,d] = selectbyname(sdI,yCol); area(t,d,FaceAlpha=0.3,FaceColor="b",DisplayName=string(yCol)); xlabel(xCol) end function compareDoses(sd1i,sd2i,y1,y2) [t1,d1] = selectbyname(sd1i,y1); [t2,d2] = selectbyname(sd2i,y2); plot(t1,d1,"b-",LineWidth=1.5); hold on plot(t2,d2,"r--",LineWidth=1.5); hold off end
