inst/doc/example-use-cases.R
In lengning/gClinBiomarker: gClinBiomarker: an R package for clinical biomarker analyses
## ----setup1, message=FALSE-----------------------------------------------
if (!require(gClinBiomarker)) {
install_github("RPackages/gClinBiomarker", host="https://github.roche.com/api/v3")
library(gClinBiomarker)
}
library(knitr)
library(devtools)
library(ggplot2)
data(input)
sample.data <- input
## ------------------------------------------------------------------------
head(sample.data)
str(sample.data)
## ------------------------------------------------------------------------
kable(
SummaryVars(data=sample.data,trt='Arm', subgroup='BEP', var=c('Age','Sex'),
var.class=c("numeric","categorical"))
)
## ------------------------------------------------------------------------
kable(
SummaryVars(data=sample.data,trt='Arm', subgroup='BEP', var=c('Age','Sex'),
var.class=c("numeric","categorical"), compare.subgroup=TRUE)
)
## ------------------------------------------------------------------------
kable(
SummaryVars(data=sample.data,trt='Arm', subgroup='BEP', var=c('Age','Sex'),
var.class=c("numeric","categorical"), test.subgroup=TRUE)
)
## ------------------------------------------------------------------------
kable(
SummaryVars(data=sample.data,trt='Arm', subgroup='BEP', var=c('Age','Sex'),
var.class=c("numeric","categorical"), trt.order=c("TRT","CTRL"))
)
## ------------------------------------------------------------------------
kable(
SummaryVars(data=sample.data, subgroup='BEP', var=c('Age','Sex'),
var.class=c("numeric","categorical"))
)
## ------------------------------------------------------------------------
sample.data$BEP2 <- ifelse(sample.data$BEP==1,"Yes","No")
kable(
SummaryVars(data=sample.data,trt='Arm', subgroup='BEP2', var=c('Age','Sex'),
var.class=c("numeric","categorical"), subgroup.indicator="Yes")
)
## ----include=TRUE,fig.width=10, fig.height=5-----------------------------
PlotProperty(data=input, biomarker.var="KRAS.exprs", biomarker.class="numeric", log2=TRUE)
## ----include=TRUE,fig.width=10, fig.height=5-----------------------------
PlotProperty(data=input, biomarker.var=NULL, biomarker.class=NULL,
var=c("Weight","Age"), var.class=c("numeric", "numeric"),
log2=c(TRUE, FALSE), par.param = list(mfrow=c(1,2), cex.axis=1.2))
## ----include=TRUE, fig.width=12, fig.height=12---------------------------
PlotProperty(data=input, biomarker.var="KRAS.exprs", biomarker.class="numeric",
var=c("ECOG", "Country"), var.class=c("categorical", "categorical"),
log2=TRUE, par.param = list(mfrow=c(3,2), cex.axis=1.2),
show.clinical.uni=TRUE)
## ----include=TRUE, fig.width=10, fig.height=12---------------------------
PlotProperty(data=input, biomarker.var="KRAS.exprs", biomarker.class="numeric",
var=c("Sex", "Age"), var.class=c("categorical", "numeric"),
log2=c(TRUE, FALSE, FALSE), par.param = list(mfrow=c(3,2), cex.axis=1.4),
show.clinical.uni=TRUE)
## ----include=TRUE, fig.width=14, fig.height=10---------------------------
PlotProperty(data=input, biomarker.var="KRAS.mutant", biomarker.class="categorical",
var="Country", var.class="categorical",
par.param = list(mfrow=c(2,2), cex.axis=1.2),
show.clinical.uni=TRUE)
## ----include=TRUE, fig.width=14, fig.height=12---------------------------
PlotProperty(data=input, biomarker.var="KRAS.mutant", biomarker.class="categorical",
var=c("Country", "Age"), var.class=c("categorical", "numeric"),
par.param = list(mfrow=c(3,2), cex.axis=1.2),
show.clinical.uni=TRUE)
## ----include=TRUE, fig.width=14, fig.height=10---------------------------
PlotProperty(data=input, biomarker.var="KRAS.mutant", biomarker.class="categorical",
var=c("Country", "Age"), var.class=c("categorical", "numeric"),
par.param = list(mfrow=c(2,2), cex.axis=1.2), show.biomarker.uni = FALSE,
show.clinical.uni=TRUE)
## ----include=TRUE, fig.width=14, fig.height=10---------------------------
PlotProperty(data=input, biomarker.var="KRAS.mutant", biomarker.class="categorical",
var=c("Country", "Age"), var.class=c("categorical", "numeric"),
par.param = list(mfrow=c(2,2), cex.axis=1.2))
## ----include=TRUE, fig.width=14, fig.height=10---------------------------
PlotProperty(data=input, biomarker.var="KRAS.mutant", biomarker.class="categorical",
var=c("Country", "Age"), var.class=c("categorical", "numeric"),
par.param = list(mfrow=c(2,2), cex.axis=1.2), show.association = FALSE,
show.clinical.uni=TRUE)
## ----include=TRUE, fig.width=14, fig.height=6----------------------------
PlotProperty(data=input, biomarker.var="KRAS.mutant", biomarker.class="categorical",
var=c("Country", "Age"), var.class=c("categorical", "numeric"),
par.param = list(mfrow=c(1,2), cex.axis=1.2),
show.biomarker.uni = FALSE)
## ----include=TRUE, fig.width=14, fig.height=6----------------------------
PlotProperty(data=input, biomarker.var="KRAS.mutant", biomarker.class="categorical",
var=c("Country", "Age"), var.class=c("categorical", "numeric"),
par.param = list(mfrow=c(1,2), cex.axis=1.1),
show.biomarker.uni = FALSE, show.association = FALSE,
show.clinical.uni = TRUE)
## ----include=TRUE, fig.width=14, fig.height=6----------------------------
PlotProperty(data=input, biomarker.var="KRAS.mutant", biomarker.class="categorical",
var=c("Country", "Age"), var.class=c("categorical", "numeric"),
par.param = list(cex.axis=1.2),
show.association = FALSE)
## ---- fig.width=4, fig.height=7------------------------------------------
PlotRspBar (input, outcome.var="Response",
rsp.levels=c("CR", "PR","SD","NON CR/PD", "PD","NE"))
## ---- fig.width=4, fig.height=7------------------------------------------
PlotRspBar (input, outcome.var="Response",
binary=TRUE,
rsp.response = c("CR","PR"),
rsp.nonresponse = c("SD", "PD","NON CR/PD","NE",NA))
## ---- fig.width=4, fig.height=7------------------------------------------
PlotRspBar (input, outcome.var="Response",
binary=TRUE,
rsp.response = c("CR","PR"),
rsp.nonresponse = c("SD", "PD","NON CR/PD","NE",NA),
col=c("green","orange"))
## ---- fig.width=7, fig.height=4------------------------------------------
PlotRspBar (input, outcome.var="Response",
binary=TRUE,
rsp.response = c("CR","PR"),
rsp.nonresponse = c("SD", "PD","NON CR/PD","NE",NA),
horiz=TRUE)
## ----fig.width=7, fig.height=7-------------------------------------------
PlotRspBar (input, outcome.var="Response",
binary=FALSE,
rsp.levels=c("CR", "PR","SD","NON CR/PD", "PD","NE"),
trt="Arm")
PlotRspBar (input, outcome.var="Response",
binary=TRUE,
rsp.response = c("CR","PR"),
rsp.nonresponse = c("SD", "PD","NON CR/PD","NE",NA),
trt="Arm")
## ----fig.width=7, fig.height=7-------------------------------------------
PlotRspBar (input, outcome.var="Response",
binary=TRUE,
rsp.response = c("CR","PR"),
rsp.nonresponse = c("SD", "PD","NON CR/PD","NE",NA),
trt="Arm", compare.bep=TRUE,bep="BEP")
## ----fig.width=7, fig.height=7-------------------------------------------
PlotRspBar (input, outcome.var="Response",
binary=TRUE,
rsp.response = c("CR","PR"),
rsp.nonresponse = c("SD", "PD","NON CR/PD","NE",NA),
trt="Arm", compare.var=TRUE,var="KRAS.mutant")
## ----fig.width=7, fig.height=7-------------------------------------------
PlotRspBar (input, outcome.var="Response",
binary=FALSE,
rsp.levels=c("CR", "PR","SD","NON CR/PD", "PD","NE"),
trt="Arm",
compare.var=TRUE,var="Sex", plot.count = TRUE)
## ----include=TRUE,fig.width=7, fig.height=7------------------------------
print(PlotKM(data=sample.data, tte="PFS",cen="PFS.event",
main="PFS ITT"))
## ----include=TRUE,fig.width=7, fig.height=7------------------------------
print(PlotKM(data=sample.data, bep="BEP",
tte="PFS",cen="PFS.event", main="PFS BEP"))
## ----include=TRUE,fig.width=7, fig.height=7------------------------------
print(PlotKM(data=sample.data, tte="PFS",cen="PFS.event",
main="PFS ITT by treatment", trt="Arm"))
## ----include=TRUE,fig.width=7, fig.height=7------------------------------
print(PlotKM(data=sample.data, tte="PFS",cen="PFS.event",
main="PFS ITT by treatment", trt="Arm",
col=c("orange","brown"),lty=c(1,2)))
## ----include=TRUE,fig.width=7, fig.height=7------------------------------
print(PlotKM(data=sample.data, tte="PFS",cen="PFS.event",
main="PFS ITT by treatment",
trt="Arm",
plot.grid = FALSE,
plot.median=T))
## ----include=TRUE,fig.width=7, fig.height=7------------------------------
print(PlotKM(data=sample.data, tte="PFS",cen="PFS.event",
main="OS BEP by treatment, by KRAS mutation",
var="KRAS.mutant"))
## ----include=TRUE,fig.width=7, fig.height=7------------------------------
print(PlotKM(data=sample.data, tte="PFS",cen="PFS.event",
main="OS BEP by treatment, by KRAS mutation",
var="KRAS.mutant", col=c("skyblue","darkgray")))
## ----include=TRUE,fig.width=7, fig.height=7------------------------------
print(PlotKM(data=sample.data, tte="PFS",cen="PFS.event",
main="OS BEP by treatment, by KRAS mutation",
trt="Arm", var="KRAS.mutant"))
## ----include=TRUE,fig.width=7, fig.height=7------------------------------
print(PlotKM(data=sample.data, tte="PFS",cen="PFS.event",
main="PFS BEP by treatment, by KRAS mutation",
trt="Arm", var="KRAS.mutant",
col=c("orange","orange","brown","brown"),
lty=c(3,1,3,1)))
## ----include=TRUE,fig.width=7, fig.height=7------------------------------
print(PlotKM(data=sample.data, tte="PFS",cen="PFS.event",
main="PFS BEP by treatment, by KRAS expression",
trt="Arm", var="KRAS.exprs", var.class="numeric",
percentile.cutoff=0.5,xlim=c(0,18))
)
## ----include=TRUE,fig.width=7, fig.height=7------------------------------
print(PlotKM(data=sample.data, tte="PFS",cen="PFS.event",
main="PFS BEP by treatment, by KRAS expression",
trt="Arm", var="KRAS.exprs", var.class="numeric",
numerical.cutoff=100)
)
## ----include=TRUE,fig.width=7, fig.height=7------------------------------
print(PlotKM(data=sample.data, tte="PFS",cen="PFS.event",
main="PFS BEP by treatment, by KRAS expression",
trt="Arm", var="KRAS.exprs", var.class="numeric",
numerical.cutoff=100, equal.in.high = F)
)
## ----include=TRUE,fig.width=7, fig.height=7------------------------------
print(PlotKM(data=sample.data, tte="PFS",cen="PFS.event",
main="PFS BEP by treatment, by KRAS expression",
trt="Arm", var="KRAS.exprs", var.class="numeric",
numerical.cutoff=c(100,500), xlim=c(0, 20))
)
## ----include=TRUE,fig.width=7, fig.height=7------------------------------
print(PlotKM(data=sample.data, tte="PFS",cen="PFS.event",
main="PFS BEP by treatment, by KRAS expression",
trt="Arm", var="KRAS.exprs", var.class="numeric",
numerical.cutoff=c(100,500),
col=c("green","green","green","brown","brown","brown"),
xlim=c(0,20))
)
## ----include=TRUE,fig.width=7, fig.height=7------------------------------
print(PlotKM(data=sample.data, tte="OS",cen="OS.event",
main="OS BEP by treatment, by KRAS mutation",
varlist=c("Arm","KRAS.mutant"),
varlist.levels=list(c("TRT","CTRL"),c("Wild Type","Mutant")),
legend.loc="left"))
## ----include=TRUE,fig.width=7, fig.height=7------------------------------
print(PlotKM(data=sample.data, tte="OS",cen="OS.event", bep="BEP",
main="OS BEP by treatment, by KRAS mutation", varlist=c("Arm","KRAS.mutant"),
varlist.levels=list(c("TRT","CTRL"),c("Wild Type","Mutant")),
varlist.labels=list(c("trt","ctrl"),c("wt","mut")),
plot.median=T,legend.loc="left"))
## ----include=TRUE,fig.width=7, fig.height=7------------------------------
print(PlotKM(data=sample.data, tte="PFS",cen="PFS.event",
var=c("Arm","KRAS.mutant"),
bep="BEP", legend.loc=NULL, legend.x=5, legend.y=.8))
## ---- fig.height=5,fig.width=7-------------------------------------------
PlotTabForestBiomarker(data=input,
outcome.class="survival",
outcome.var=c("PFS","PFS.event"),
trt="Arm",
var="KRAS.mutant",
var.class="categorical")
## ---- fig.height=10,fig.width=9------------------------------------------
PlotTabForestBiomarker(data=input,
outcome.class="survival",
outcome.var=c("PFS","PFS.event"),
trt="Arm",
var="KRAS.mutant",
var.class="categorical",
tabforest = TRUE)
## ---- fig.height=5,fig.width=7-------------------------------------------
PlotTabForestBiomarker(data=input,
outcome.class="survival",
outcome.var=c("PFS","PFS.event"),
trt="Arm",
var="KRAS.mutant",
var.class="categorical",
bep = 'BEP',
bep.indicator=1)
## ---- fig.height=4,fig.width=6-------------------------------------------
PlotTabForestBiomarker(data=input,
outcome.class="survival",
outcome.var=c("PFS","PFS.event"),
trt="Arm",
var="KRAS.mutant",
var.class="categorical",
var.name="KRAS mut",
show.itt=FALSE,
show.bep=FALSE)
## ---- fig.height=6,fig.width=9-------------------------------------------
PlotTabForestBiomarker(data=input,
outcome.class="survival",
outcome.var=c("PFS","PFS.event"),
trt="Arm",
var="KRAS.exprs",
var.class="numeric", var.name="KRAS exprs",
percentile.cutoff=c(.25,.5,.75),
# cols=c("black","black","darkgreen","darkgreen","darkgreen"),
numerical.cutoff=NULL,
greater=TRUE, less=FALSE,
within.bin=FALSE,
show.itt=TRUE, show.bep=TRUE)
## ---- fig.height=6,fig.width=9-------------------------------------------
PlotTabForestBiomarker(data=input,
outcome.class="survival",
outcome.var=c("PFS","PFS.event"),
trt="Arm",
var="KRAS.exprs",
var.class="numeric", var.name="KRAS exprs",
percentile.cutoff=c(.25,.5,.75),
numerical.cutoff=NULL,
greater=FALSE, less=TRUE,
within.bin=FALSE,
show.itt=TRUE, show.bep=TRUE,
bep = 'BEP', bep.indicator=1)
## ---- fig.height=6,fig.width=9-------------------------------------------
PlotTabForestBiomarker(data=input,
outcome.class="survival",
outcome.var=c("PFS","PFS.event"),
trt="Arm",
var="KRAS.exprs",
var.class="numeric", var.name="KRAS exprs",
percentile.cutoff=c(.25,.5,.75),
numerical.cutoff=NULL,
greater=TRUE, less=TRUE,
within.bin=FALSE,
show.itt=TRUE, show.bep=TRUE)
## ---- fig.height=6,fig.width=9-------------------------------------------
PlotTabForestBiomarker(data=input,
outcome.class="survival",
outcome.var=c("PFS","PFS.event"),
trt="Arm",
var="KRAS.exprs",
var.class="numeric", var.name="KRAS exprs",
percentile.cutoff=c(.25,.5,.75),
numerical.cutoff=NULL,
greater=TRUE, less=TRUE, greater.by.less = TRUE,
within.bin=FALSE,
show.itt=TRUE, show.bep=TRUE)
## ---- fig.height=6,fig.width=9-------------------------------------------
PlotTabForestBiomarker(data=input,
outcome.class="survival",
outcome.var=c("PFS","PFS.event"),
trt="Arm",
var="KRAS.exprs",
var.class="numeric", var.name="KRAS exprs",
percentile.cutoff=c(.25,.5,.75),
numerical.cutoff=NULL,
greater=FALSE, less=FALSE,
within.bin=TRUE,
show.itt=TRUE, show.bep=TRUE)
## ---- fig.height=6,fig.width=9-------------------------------------------
PlotTabForestBiomarker(data=input,
outcome.class="survival",
outcome.var=c("PFS","PFS.event"),
trt="Arm",
var="KRAS.exprs",
var.class="numeric", var.name="KRAS exprs",
percentile.cutoff=NULL,
numerical.cutoff=c(50,100),
greater=TRUE, less=FALSE,
within.bin=FALSE,
show.itt=TRUE, show.bep=TRUE)
## ---- fig.height=6,fig.width=9-------------------------------------------
PlotTabForestBiomarker(data=input,
outcome.class="survival",
outcome.var=c("PFS","PFS.event"),
trt="Arm",
var="KRAS.exprs",
var.class="numeric", var.name="KRAS exprs",
percentile.cutoff=NULL,
numerical.cutoff=c(50,100),
greater=TRUE, less=FALSE,
within.bin=FALSE,
show.itt=TRUE, show.bep=TRUE,
bep = 'BEP', bep.indicator=1, covariate="Age")
## ---- fig.height=6,fig.width=9-------------------------------------------
PlotTabForestBiomarker(data=input,
outcome.class="survival",
outcome.var=c("PFS","PFS.event"),
trt="Arm",
var="KRAS.exprs",
var.class="numeric", var.name="KRAS exprs",
percentile.cutoff=NULL,
numerical.cutoff=c(50,100),
greater=TRUE, less=FALSE,
within.bin=FALSE,
show.itt=TRUE, show.bep=TRUE,
bep = 'BEP', bep.indicator=1, strata="Sex")
## ---- fig.height=6,fig.width=9-------------------------------------------
PlotTabForestBiomarker(data=input,
outcome.class="survival",
outcome.var=c("PFS","PFS.event"),
trt="Arm",
var="KRAS.exprs",
var.class="numeric", var.name="KRAS exprs",
percentile.cutoff=NULL,
numerical.cutoff=c(50,100),
greater=TRUE, less=FALSE,
within.bin=FALSE,
show.itt=TRUE, show.bep=TRUE,
bep = 'BEP', bep.indicator=1,covariate="Age",strata="Sex")
## ---- fig.height=4,fig.width=6-------------------------------------------
PlotTabForestBiomarker(data=subset(input, Arm=="TRT"),
outcome.class="survival",
outcome.var=c("PFS","PFS.event"),
trt=NULL,
var="KRAS.exprs",
var.class="numeric", var.name="KRAS exprs",
percentile.cutoff=NULL,
numerical.cutoff=c(50,100),
greater=TRUE, less=FALSE,
within.bin=FALSE,
show.itt=TRUE, show.bep=TRUE,covariate="Age",strata="Sex")
## ---- fig.height=6,fig.width=9-------------------------------------------
PlotTabForestBiomarker(data=input,
outcome.class="survival",
outcome.var=c("PFS","PFS.event"),
trt="Arm",
var="KRAS.exprs",
var.class="numeric", var.name="KRAS exprs",
percentile.cutoff=c(.25,.5,.75),
numerical.cutoff=NULL,
greater=TRUE, less=FALSE,
within.bin=FALSE,
show.itt=TRUE, show.bep=TRUE,
covariate=NULL, #Sex
strata=NULL, #Age
placebo.code='TRT',
active.code='CTRL')
## ---- fig.height=12,fig.width=9------------------------------------------
PlotTabForestBiomarker(data=input,
outcome.class="survival",
outcome.var=c("PFS","PFS.event"),
trt="Arm",
var="KRAS.exprs",
var.class="numeric", var.name="KRAS exprs",
percentile.cutoff=c(.25,.5,.75),
numerical.cutoff=NULL,
greater=TRUE, less=FALSE,
within.bin=FALSE,
show.itt=TRUE, show.bep=TRUE,
across.and.within = TRUE)
## ---- fig.height=5,fig.width=7-------------------------------------------
PlotTabForestBiomarker(data=input,
outcome.class="binary",
outcome.var=c("Response"),
rsp.cat = TRUE,
rsp.response = c("CR","PR"),
rsp.nonresponse = c("SD", "PD","NON CR/PD","NE",NA),
trt="Arm",
var="KRAS.mutant",
var.class="categorical")
## ---- fig.height=10,fig.width=9------------------------------------------
PlotTabForestBiomarker(data=input,
outcome.class="binary",
outcome.var=c("Response"),
rsp.cat = TRUE,
rsp.response = c("CR","PR"),
rsp.nonresponse = c("SD", "PD","NON CR/PD","NE",NA),
trt="Arm",
var="KRAS.mutant",
var.class="categorical",
tabforest = TRUE)
## ---- fig.height=5,fig.width=7-------------------------------------------
PlotTabForestBiomarker(data=input,
outcome.class="continuous",
outcome.var=c("Lab_ontrt"),
trt="Arm",
var="KRAS.mutant",
var.class="categorical")
## ---- fig.height=10,fig.width=10-----------------------------------------
PlotTabForestBiomarker(data=input,
outcome.class="continuous",
outcome.var=c("Lab_ontrt"),
trt="Arm",
var="KRAS.mutant",
var.class="categorical",tabforest=T)
## ---- fig.height=12,fig.width=9------------------------------------------
PlotTabForestMulti(data=input,
outcome.class="survival",
outcome.var=c("PFS","PFS.event"),
trt="Arm",
var=c("Sex","Age"),
bep="BEP",bep.indicator=1,
compare.bep.itt=TRUE
)
## ---- fig.height=6,fig.width=9-------------------------------------------
PlotTabForestMulti(data=input,
outcome.class="survival",
outcome.var=c("PFS","PFS.event"),
trt="Arm",
var=c("Sex","Age"),
bep="BEP",bep.indicator=1, compare.bep.itt=FALSE,
compare.subgroup=TRUE, subgroup="KRAS.mutant"
)
## ---- fig.height=6,fig.width=9-------------------------------------------
PlotTabForestMulti(data=input,
outcome.class="survival",
outcome.var=c("PFS","PFS.event"),
trt="Arm",
var=c("Sex","Age"),
bep="BEP",bep.indicator=1, compare.bep.itt=FALSE,
compare.subgroup=TRUE, subgroup="KRAS.mutant", show.itt=TRUE
)
## ---- fig.height=12,fig.width=9------------------------------------------
PlotTabForestMulti(data=input,
outcome.class="survival",
outcome.var=c("PFS","PFS.event"),
trt="Arm",
var=c("Sex","Age"),
bep="BEP",bep.indicator=1, compare.bep.itt=FALSE,
compare.subgroup=TRUE, subgroup="KRAS.mutant", show.itt=TRUE, show.bep=TRUE
)
## ---- fig.height=12,fig.width=9------------------------------------------
PlotTabForestMulti(data=input,
outcome.class="survival",
outcome.var=c("PFS","PFS.event"),
trt="Arm",
var=c("Sex","Age"), compare.bep.itt=FALSE,
compare.subgroup=TRUE, subgroup="KRAS.mutant", show.itt=TRUE, show.bep=TRUE
)
## ---- fig.height=6,fig.width=9-------------------------------------------
PlotTabForestMulti(data=subset(input,Arm=="TRT"),
outcome.class="survival",
outcome.var=c("PFS","PFS.event"),
trt=NULL,
var=c("Sex","Age"),
bep="BEP",bep.indicator=1, compare.bep.itt=TRUE
)
## ---- fig.height=12,fig.width=9------------------------------------------
PlotTabForestMulti(data=input,
outcome.class="survival",
outcome.var=c("PFS","PFS.event"),
trt="Arm", percentile.cutoff=c(.33,.66),
var=c("Sex","Age"),
bep="BEP",bep.indicator=1, compare.bep.itt=FALSE,
compare.subgroup=TRUE, subgroup="KRAS.mutant"
)
## ---- fig.height=12,fig.width=9------------------------------------------
PlotTabForestMulti(data=input,
outcome.class="survival",
outcome.var=c("PFS","PFS.event"),
trt="Arm", percentile.cutoff=c(.33,.66),less=TRUE,greater=FALSE,
var=c("Sex","Age"),
bep="BEP",bep.indicator=1, compare.bep.itt=FALSE,
compare.subgroup=TRUE, subgroup="KRAS.mutant"
)
## ---- fig.height=8,fig.width=9-------------------------------------------
PlotTabForestMulti(data=input,
outcome.class="survival",
outcome.var=c("PFS","PFS.event"),
trt="Arm", percentile.cutoff=c(.33,.66),within.bin=TRUE,
var=c("Sex","Age"),
bep="BEP",bep.indicator=1, compare.bep.itt=FALSE,
compare.subgroup=TRUE, subgroup="KRAS.mutant"
)
## ---- fig.height=6,fig.width=9-------------------------------------------
PlotTabForestMulti(data=input,
outcome.class="survival",
outcome.var=c("PFS","PFS.event"),
trt="Arm",
var=c("Sex","Age"),
compare.bep.itt=FALSE, compare.subgroup=FALSE,itt.name=""
)
## ---- fig.height=6,fig.width=9-------------------------------------------
PlotTabForestMulti(data=input,
outcome.class="binary",
outcome.var=c("Response"),
rsp.cat = TRUE,
rsp.response = c("CR","PR"),
rsp.nonresponse = c("SD", "PD","NON CR/PD","NE",NA),
trt="Arm",
var=c("Sex","Age"),
compare.bep.itt=FALSE, compare.subgroup=FALSE,itt.name=""
)
## ---- fig.height=10,fig.width=10-----------------------------------------
PlotTabForestMulti(data=input,
outcome.class="binary",
outcome.var=c("Response"),
rsp.cat = TRUE,
rsp.response = c("CR","PR"),
rsp.nonresponse = c("SD", "PD","NON CR/PD","NE",NA),
trt="Arm",
var=c("Sex","Age"),
compare.bep.itt=FALSE, compare.subgroup=FALSE,itt.name="", tabforest=T
)
## ---- fig.height=6,fig.width=9-------------------------------------------
PlotTabForestMulti(data=input,
outcome.class="continuous",
outcome.var=c("Lab_ontrt"),
trt="Arm",
var=c("Sex","Age"),
compare.bep.itt=FALSE, compare.subgroup=FALSE,itt.name=""
)
## ---- fig.height=10,fig.width=10-----------------------------------------
PlotTabForestMulti(data=input,
outcome.class="continuous",
outcome.var=c("Lab_ontrt"),
trt="Arm",
var=c("Sex","Age"),
compare.bep.itt=FALSE, compare.subgroup=FALSE,itt.name="", tabforest=T
)
## ------------------------------------------------------------------------
PlotSTEPP(data = input,
outcome.var = c("PFS", "PFS.event"),
outcome.class = "survival",
trt = "Arm",
var = "KRAS.exprs",
placebo.code = "CTRL",
active.code = "TRT",
csv.name = NULL,
pdf.name = NULL
)
## ------------------------------------------------------------------------
PlotSTEPP(data = input,
outcome.var = "Baseline.SLD",
outcome.class = "continuous",
trt = "Arm",
var = "KRAS.exprs",
covariate= "Sex",
placebo.code = "CTRL",
active.code = "TRT",
csv.name = NULL,
pdf.name = NULL
)
## ------------------------------------------------------------------------
PlotSTEPP(data = input,
outcome.var = "ECOG",
outcome.class = "binary",
trt = "Arm",
var = "KRAS.exprs",
placebo.code = "CTRL",
active.code = "TRT",
csv.name = NULL,
pdf.name = NULL
)
## ------------------------------------------------------------------------
CoxTab(data=sample.data, tte="OS", cens="OS.event",bep='BEP', var='Sex' )
## ------------------------------------------------------------------------
kable(
CoxTab(data=sample.data,tte="OS", cens="OS.event", var=c('Sex',"Country","Age"),
var.class=c("categorical","categorical","numeric"))
)
## ------------------------------------------------------------------------
kable(
CoxTab(data=sample.data,tte="OS", cens="OS.event", var=c('Sex',"Country","Age"))
)
## ------------------------------------------------------------------------
kable(
CoxTab(data=sample.data,tte="OS", cens="OS.event", var=c('Sex',"Country","Age"),
var.class=c("categorical","categorical","numeric"), bep="BEP")
)
## ------------------------------------------------------------------------
kable(
CoxTab(data=sample.data,tte="OS", cens="OS.event", var=c('Sex',"Country","Age"),
var.class=c("ordered.factor","categorical","numeric"),
ordered.factor.levels.list=list(Sex=c("M","F")),bep="BEP")
)
## ------------------------------------------------------------------------
kable(
CoxTab(data=sample.data,tte="OS", cens="OS.event", var=c('Sex',"Country","Age"),
additive=FALSE)
)
## ------------------------------------------------------------------------
SummaryTwoGroups(outcome.var = input$OS, treatment.var = input$Arm,
placebo.code = "CTRL", active.code = "TRT",
outcome.class = "continuous")
## ------------------------------------------------------------------------
SummaryTwoGroups(outcome.var = input$OS, treatment.var = input$Arm,
placebo.code = "CTRL", active.code = "TRT",
outcome.class = "continuous", covariate.var = input$Sex)
## ------------------------------------------------------------------------
SummaryTwoGroups(outcome.var = input$OS, treatment.var = input$Arm,
placebo.code = "CTRL", active.code = "TRT",
outcome.class = "continuous", covariate.var = input$Sex,
return.fit = TRUE)
## ------------------------------------------------------------------------
SummaryTwoGroups(outcome.var = input$OS.event, treatment.var = input$Arm,
placebo.code = "CTRL", active.code = "TRT",
outcome.class = "binary")
## ------------------------------------------------------------------------
SummaryTwoGroups(outcome.var = input[, c("OS", "OS.event")],
treatment.var = input$Arm, placebo.code = "CTRL",
active.code = "TRT", outcome.class = "survival")
## ------------------------------------------------------------------------
SummaryTwoGroups(outcome.var = input[, c("OS", "OS.event")],
treatment.var = input$Arm, placebo.code = "CTRL",
active.code = "TRT", outcome.class = "survival",
covariate.var = input$Sex)
## ------------------------------------------------------------------------
SummaryTwoGroups(outcome.var = input[, c("OS", "OS.event")],
treatment.var = input$Arm, placebo.code = "CTRL",
active.code = "TRT", outcome.class = "survival",
covariate.var = input$Sex, strat.factor.var = input$Age)
## ------------------------------------------------------------------------
kable(
LogRankTab(data=input,tte="PFS",cens="PFS.event",var="Arm")
)
## ------------------------------------------------------------------------
example <- data.frame( y=c(rnorm(30)+10, rnorm(4)+20, rnorm(15)+15, NA),
time=c(rep("t2", 30), rep("t4",4), rep("t1", 15), "t3"),
grp=sample(1:3, 50, TRUE), sex=sample(1:2, 50, TRUE))
head(example)
str(example)
## ----include=TRUE,fig.width=7, fig.height=4------------------------------
BoxPlot(list(a=rnorm(50,,3), b=rnorm(25,1,4), c=rnorm(75,2,1)))
## ----include=TRUE,fig.width=7, fig.height=4------------------------------
BoxPlot(list(a=rnorm(50,,3), b=rnorm(25,1,4), c=rnorm(75,2,1)), horizontal=TRUE,
Xaxis=list(las=2, hadj=2), Xaxis2=list(las=2, hadj=-.25))
## ----include=TRUE,fig.width=7, fig.height=4------------------------------
BoxPlot(matrix(rnorm(100), ncol=4, dimnames=list(NULL, LETTERS[1:4])) )
## ----include=TRUE,fig.width=7, fig.height=4------------------------------
BoxPlot(rnorm(50,,3), rnorm(25,1,2), rnorm(75,2,1))
## ----include=TRUE,fig.width=7, fig.height=4------------------------------
BoxPlot(rnorm(50,,3), rnorm(25,1,2), rnorm(75,2,1), horizontal=TRUE)
## ----include=TRUE,fig.width=7, fig.height=4------------------------------
BoxPlot(example, y~time, sc.pch=16)
## ----include=TRUE,fig.width=7, fig.height=4------------------------------
BoxPlot(example, y~time, sc.pch=16, box.type="bp")
## ----include=TRUE,fig.width=7, fig.height=4------------------------------
BoxPlot(example, y~time, sc.pch=16, box.type="bp", Title=list(main="Custom Main Title"))
## ----include=TRUE,fig.width=7, fig.height=4------------------------------
BoxPlot(example, y~time, trend="median", ylab="Y-Axis Label")
## ----include=TRUE,fig.width=7, fig.height=4------------------------------
BoxPlot(example, y~time, trend="median", ylab="Y-Axis Label",
sc.col=c("red", "blue", "green")[example$grp] )
## ----include=TRUE,fig.width=7, fig.height=4------------------------------
BoxPlot(example, y~time, trend="median", ylab="Y-Axis Label",
sc.col=c("red", "blue", "green")[example$grp],
sc.pch=c(5,10)[example$sex] )
legend("bottomright", fill=c("red", "green", "blue", "white", "white"),
legend=c("Stage I", "Stage II", "Stage III", "Female", "Male"),
pch=c(-1, -1, -1, 5, 10), border=NA)
## ----include=TRUE,fig.width=7, fig.height=4------------------------------
example2 <- data.frame(y1=12+rnorm(15), y2=15+rnorm(15), y3=25+rnorm(15))
## ----include=TRUE,fig.width=7, fig.height=4------------------------------
BoxPlot(example2, var=c("y1", "y2", "y3"), Grid=TRUE, trend="mean")
## ----include=TRUE,fig.width=7, fig.height=4------------------------------
BoxPlot(example2, var=c("y1", "y2", "y3"), box.type="bp", Grid=TRUE)
## ----include=TRUE,fig.width=7, fig.height=4------------------------------
BoxPlot(rnorm(1856, 5), runif(1245, 2,10), exp(rnorm(2311)), sc.col=as.rgb("black", .05),
box.type="bp", Xaxis=list(labels=c("~N(5,1)", "~Unif(2,10)", "~exp(N(0,1))")), ylim=c(0,15))
## ----include=TRUE,fig.width=7, fig.height=4------------------------------
mat <- matrix(c(rep(10,45), rep(15,45), rep(35,45))+rnorm(135), ncol=3)
BoxPlot(mat, trend="mean", trend.col="red", Ylabel=list(text="Example Measurements"))
## ----include=TRUE,fig.width=7, fig.height=4------------------------------
data(mtcars)
BoxPlot(mtcars, mpg~gear:cyl)
## ----include=TRUE,fig.width=7, fig.height=4------------------------------
BoxPlot(mtcars, mpg~cyl %in% gear)
## ----include=TRUE,fig.width=7, fig.height=4------------------------------
dat <- mtcars
dat$cyl <- factor(dat$cyl, levels=c(4,6,8), labels=c("4Cyl", "6Cyl", "8Cyl"))
dat$gear <- factor(dat$gear, levels=c(3,4,5), labels=c("3Gear", "4Gear", "5Gear"))
BoxPlot(dat, mpg~cyl %in% gear)
## ----include=TRUE,fig.width=7, fig.height=4------------------------------
BoxPlot(dat, mpg~cyl:gear, XaxisTab=list(),mar=c(8,3,5,1))
## ----include=TRUE,fig.width=7, fig.height=4------------------------------
BoxPlot(mtcars, mpg~cyl:gear, XaxisTab=list(), mar=c(5,8,5,4),
horizontal=TRUE, Ylabel=list(text="Y-axis label now appearing on X-axis"))
## ----include=TRUE,fig.width=7, fig.height=4------------------------------
BoxPlot(dat, mpg~cyl:gear, XaxisTab=list(font=2, col="darkblue", cex=1.25), mar=c(5,3,5,1))
## ----include=TRUE,fig.width=7, fig.height=4------------------------------
BoxPlot(dat, mpg~cyl:gear, XaxisTab=list(Label=list(font=2, col="darkblue", cex=1.25),
Text=list(col="red")), mar=c(5,3,5,1))
## ----include=TRUE,fig.width=7, fig.height=4------------------------------
BoxPlot(dat, mpg~cyl:gear:vs, XaxisTab=list(), mar=c(5,3,5,1))
## ----include=TRUE,fig.width=7, fig.height=4------------------------------
BoxPlot(mtcars, mpg~cyl %in% gear,
Xaxis=list(labels=paste(rep(c("4Cyl", "6Cyl", "8Cyl"),3),
c(rep("3Gear",3), rep("4Gear",3), rep("5Gear",3)), sep=".")))
## ----include=TRUE,fig.width=7, fig.height=4------------------------------
BoxPlot(dat, mpg~cyl %in% gear, Title=list(main="Miles per Gallon by Number of Gears",
col.main="Green", cex.main=2.5), vline=c(3.5, 6.5), vl.lty=2, vl.col="gray", vl.lwd=2,
Xaxis=list(labels=NA, at=1:9, tick=TRUE), col=c(rep("blue", 3), rep("red", 3), rep("green", 3)),
Xaxis2=list(tick=FALSE), Yaxis=list(at=seq(10,34,2)), Grid=list(x=1:9, y=seq(10,34,2)),
Xlabel=list(text=paste(rep(c("4Cyl", "6Cyl", "8Cyl"),3), c(rep("3Gear",3), rep("4Gear",3), rep("5Gear",3))),
at=1:9, las=2, adj=1, line=0.75, col=c(rep("blue", 3), rep("red", 3), rep("green", 3))),
mean.col=c(rep("cyan", 3), rep("orange", 3), rep("magenta", 3)), Box=FALSE, trend="mean",mar=c(6,4,5,2) )
## ----include=TRUE,fig.width=7, fig.height=4------------------------------
BoxPlot(mtcars, mpg~cyl %in% gear, Title=list(main="Miles per Gallon by Number of Gears", col.main="#84d52b", cex.main=1.5),
vline=c(3.5, 6.5), vl.lty=2, vl.col="gray", vl.lwd=2,
Xaxis2=list(tick=FALSE, las=2, hadj=-.25), Yaxis=list(at=seq(10,34,2)), Grid=list(x=1:9, y=seq(10,34,2)),
mean.col=c(rep("cyan", 3), rep("orange", 3), rep("magenta", 3)), Box=FALSE, trend="mean",
mar=c(3, 7, 4, 4), horizontal=TRUE, sc.pch=c(0, 15)[dat$am+1], sc.col="wheat4",
XaxisTab=list(Text=list(col=c(rep("cyan", 3), rep("orange", 3), rep("magenta", 3)))) )
legend(x="topright", pch=c(0, 15), legend=c("automatic", "manual"), box.lty=0, col="wheat4")
## ------------------------------------------------------------------------
PlotLong(longbmkr, aes(x=vm, y=ep),
xlab = 'Visitation Month',
ylab = 'Biomarker Endpoint',
labs.title = 'Mean +/- SEM')
## ------------------------------------------------------------------------
PlotLong(longbmkr, aes(x=vm, y=ep), fun.data = 'tukey',
xlab = 'Visitation Month',
ylab = 'Biomarker Endpoint',
labs.title = 'Tukey Whiskers and Hinges')
## ------------------------------------------------------------------------
PlotLong(longbmkr, aes(x=vm, y=ep, group=trt, color=trt, fill=trt),
fun.data = 'tukey', facet.fun = . ~ sex,
xlab = 'Visitation Month',
ylab = 'Biomarker Endpoint',
labs.title = 'Biomarker Timecourse',
labs.caption = 'Ribbons represent Tukey hinges and whiskers')
## ---- fig.height = 3.5,eval=TRUE-----------------------------------------
library(dplyr)
PlotLong(longbmkr %>% filter(vm <= 24),
aes(x=vm, y=ep, group=trt, color=trt, fill=trt),
fun.data = 'tukey', facet.fun = . ~ sex,
show.counts = 'table',
xlab = 'Visitation Month',
ylab = 'Biomarker Endpoint',
labs.title = 'Biomarker Timecourse',
labs.caption = 'Ribbons represent Tukey hinges and whiskers')
## ---- fig.height = 3.5, eval=TRUE----------------------------------------
PlotLong(longbmkr %>% filter(vm <= 24),
aes(x=vm, y=ep, group=trt, color=trt, fill=trt),
fun.data = 'tukey', facet.fun = . ~ sex,
show.counts = 'table',
plot.style = 'errorbars',
xlab = 'Visitation Month',
ylab = 'Biomarker Endpoint',
labs.title = 'Biomarker Timecourse',
labs.caption = 'Ribbons represent Tukey hinges and whiskers')
lengning/gClinBiomarker documentation built on May 9, 2019, 2:55 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
## ----setup1, message=FALSE-----------------------------------------------
if (!require(gClinBiomarker)) {
install_github("RPackages/gClinBiomarker", host="https://github.roche.com/api/v3")
library(gClinBiomarker)
}
library(knitr)
library(devtools)
library(ggplot2)
data(input)
sample.data <- input
## ------------------------------------------------------------------------
head(sample.data)
str(sample.data)
## ------------------------------------------------------------------------
kable(
SummaryVars(data=sample.data,trt='Arm', subgroup='BEP', var=c('Age','Sex'),
var.class=c("numeric","categorical"))
)
## ------------------------------------------------------------------------
kable(
SummaryVars(data=sample.data,trt='Arm', subgroup='BEP', var=c('Age','Sex'),
var.class=c("numeric","categorical"), compare.subgroup=TRUE)
)
## ------------------------------------------------------------------------
kable(
SummaryVars(data=sample.data,trt='Arm', subgroup='BEP', var=c('Age','Sex'),
var.class=c("numeric","categorical"), test.subgroup=TRUE)
)
## ------------------------------------------------------------------------
kable(
SummaryVars(data=sample.data,trt='Arm', subgroup='BEP', var=c('Age','Sex'),
var.class=c("numeric","categorical"), trt.order=c("TRT","CTRL"))
)
## ------------------------------------------------------------------------
kable(
SummaryVars(data=sample.data, subgroup='BEP', var=c('Age','Sex'),
var.class=c("numeric","categorical"))
)
## ------------------------------------------------------------------------
sample.data$BEP2 <- ifelse(sample.data$BEP==1,"Yes","No")
kable(
SummaryVars(data=sample.data,trt='Arm', subgroup='BEP2', var=c('Age','Sex'),
var.class=c("numeric","categorical"), subgroup.indicator="Yes")
)
## ----include=TRUE,fig.width=10, fig.height=5-----------------------------
PlotProperty(data=input, biomarker.var="KRAS.exprs", biomarker.class="numeric", log2=TRUE)
## ----include=TRUE,fig.width=10, fig.height=5-----------------------------
PlotProperty(data=input, biomarker.var=NULL, biomarker.class=NULL,
var=c("Weight","Age"), var.class=c("numeric", "numeric"),
log2=c(TRUE, FALSE), par.param = list(mfrow=c(1,2), cex.axis=1.2))
## ----include=TRUE, fig.width=12, fig.height=12---------------------------
PlotProperty(data=input, biomarker.var="KRAS.exprs", biomarker.class="numeric",
var=c("ECOG", "Country"), var.class=c("categorical", "categorical"),
log2=TRUE, par.param = list(mfrow=c(3,2), cex.axis=1.2),
show.clinical.uni=TRUE)
## ----include=TRUE, fig.width=10, fig.height=12---------------------------
PlotProperty(data=input, biomarker.var="KRAS.exprs", biomarker.class="numeric",
var=c("Sex", "Age"), var.class=c("categorical", "numeric"),
log2=c(TRUE, FALSE, FALSE), par.param = list(mfrow=c(3,2), cex.axis=1.4),
show.clinical.uni=TRUE)
## ----include=TRUE, fig.width=14, fig.height=10---------------------------
PlotProperty(data=input, biomarker.var="KRAS.mutant", biomarker.class="categorical",
var="Country", var.class="categorical",
par.param = list(mfrow=c(2,2), cex.axis=1.2),
show.clinical.uni=TRUE)
## ----include=TRUE, fig.width=14, fig.height=12---------------------------
PlotProperty(data=input, biomarker.var="KRAS.mutant", biomarker.class="categorical",
var=c("Country", "Age"), var.class=c("categorical", "numeric"),
par.param = list(mfrow=c(3,2), cex.axis=1.2),
show.clinical.uni=TRUE)
## ----include=TRUE, fig.width=14, fig.height=10---------------------------
PlotProperty(data=input, biomarker.var="KRAS.mutant", biomarker.class="categorical",
var=c("Country", "Age"), var.class=c("categorical", "numeric"),
par.param = list(mfrow=c(2,2), cex.axis=1.2), show.biomarker.uni = FALSE,
show.clinical.uni=TRUE)
## ----include=TRUE, fig.width=14, fig.height=10---------------------------
PlotProperty(data=input, biomarker.var="KRAS.mutant", biomarker.class="categorical",
var=c("Country", "Age"), var.class=c("categorical", "numeric"),
par.param = list(mfrow=c(2,2), cex.axis=1.2))
## ----include=TRUE, fig.width=14, fig.height=10---------------------------
PlotProperty(data=input, biomarker.var="KRAS.mutant", biomarker.class="categorical",
var=c("Country", "Age"), var.class=c("categorical", "numeric"),
par.param = list(mfrow=c(2,2), cex.axis=1.2), show.association = FALSE,
show.clinical.uni=TRUE)
## ----include=TRUE, fig.width=14, fig.height=6----------------------------
PlotProperty(data=input, biomarker.var="KRAS.mutant", biomarker.class="categorical",
var=c("Country", "Age"), var.class=c("categorical", "numeric"),
par.param = list(mfrow=c(1,2), cex.axis=1.2),
show.biomarker.uni = FALSE)
## ----include=TRUE, fig.width=14, fig.height=6----------------------------
PlotProperty(data=input, biomarker.var="KRAS.mutant", biomarker.class="categorical",
var=c("Country", "Age"), var.class=c("categorical", "numeric"),
par.param = list(mfrow=c(1,2), cex.axis=1.1),
show.biomarker.uni = FALSE, show.association = FALSE,
show.clinical.uni = TRUE)
## ----include=TRUE, fig.width=14, fig.height=6----------------------------
PlotProperty(data=input, biomarker.var="KRAS.mutant", biomarker.class="categorical",
var=c("Country", "Age"), var.class=c("categorical", "numeric"),
par.param = list(cex.axis=1.2),
show.association = FALSE)
## ---- fig.width=4, fig.height=7------------------------------------------
PlotRspBar (input, outcome.var="Response",
rsp.levels=c("CR", "PR","SD","NON CR/PD", "PD","NE"))
## ---- fig.width=4, fig.height=7------------------------------------------
PlotRspBar (input, outcome.var="Response",
binary=TRUE,
rsp.response = c("CR","PR"),
rsp.nonresponse = c("SD", "PD","NON CR/PD","NE",NA))
## ---- fig.width=4, fig.height=7------------------------------------------
PlotRspBar (input, outcome.var="Response",
binary=TRUE,
rsp.response = c("CR","PR"),
rsp.nonresponse = c("SD", "PD","NON CR/PD","NE",NA),
col=c("green","orange"))
## ---- fig.width=7, fig.height=4------------------------------------------
PlotRspBar (input, outcome.var="Response",
binary=TRUE,
rsp.response = c("CR","PR"),
rsp.nonresponse = c("SD", "PD","NON CR/PD","NE",NA),
horiz=TRUE)
## ----fig.width=7, fig.height=7-------------------------------------------
PlotRspBar (input, outcome.var="Response",
binary=FALSE,
rsp.levels=c("CR", "PR","SD","NON CR/PD", "PD","NE"),
trt="Arm")
PlotRspBar (input, outcome.var="Response",
binary=TRUE,
rsp.response = c("CR","PR"),
rsp.nonresponse = c("SD", "PD","NON CR/PD","NE",NA),
trt="Arm")
## ----fig.width=7, fig.height=7-------------------------------------------
PlotRspBar (input, outcome.var="Response",
binary=TRUE,
rsp.response = c("CR","PR"),
rsp.nonresponse = c("SD", "PD","NON CR/PD","NE",NA),
trt="Arm", compare.bep=TRUE,bep="BEP")
## ----fig.width=7, fig.height=7-------------------------------------------
PlotRspBar (input, outcome.var="Response",
binary=TRUE,
rsp.response = c("CR","PR"),
rsp.nonresponse = c("SD", "PD","NON CR/PD","NE",NA),
trt="Arm", compare.var=TRUE,var="KRAS.mutant")
## ----fig.width=7, fig.height=7-------------------------------------------
PlotRspBar (input, outcome.var="Response",
binary=FALSE,
rsp.levels=c("CR", "PR","SD","NON CR/PD", "PD","NE"),
trt="Arm",
compare.var=TRUE,var="Sex", plot.count = TRUE)
## ----include=TRUE,fig.width=7, fig.height=7------------------------------
print(PlotKM(data=sample.data, tte="PFS",cen="PFS.event",
main="PFS ITT"))
## ----include=TRUE,fig.width=7, fig.height=7------------------------------
print(PlotKM(data=sample.data, bep="BEP",
tte="PFS",cen="PFS.event", main="PFS BEP"))
## ----include=TRUE,fig.width=7, fig.height=7------------------------------
print(PlotKM(data=sample.data, tte="PFS",cen="PFS.event",
main="PFS ITT by treatment", trt="Arm"))
## ----include=TRUE,fig.width=7, fig.height=7------------------------------
print(PlotKM(data=sample.data, tte="PFS",cen="PFS.event",
main="PFS ITT by treatment", trt="Arm",
col=c("orange","brown"),lty=c(1,2)))
## ----include=TRUE,fig.width=7, fig.height=7------------------------------
print(PlotKM(data=sample.data, tte="PFS",cen="PFS.event",
main="PFS ITT by treatment",
trt="Arm",
plot.grid = FALSE,
plot.median=T))
## ----include=TRUE,fig.width=7, fig.height=7------------------------------
print(PlotKM(data=sample.data, tte="PFS",cen="PFS.event",
main="OS BEP by treatment, by KRAS mutation",
var="KRAS.mutant"))
## ----include=TRUE,fig.width=7, fig.height=7------------------------------
print(PlotKM(data=sample.data, tte="PFS",cen="PFS.event",
main="OS BEP by treatment, by KRAS mutation",
var="KRAS.mutant", col=c("skyblue","darkgray")))
## ----include=TRUE,fig.width=7, fig.height=7------------------------------
print(PlotKM(data=sample.data, tte="PFS",cen="PFS.event",
main="OS BEP by treatment, by KRAS mutation",
trt="Arm", var="KRAS.mutant"))
## ----include=TRUE,fig.width=7, fig.height=7------------------------------
print(PlotKM(data=sample.data, tte="PFS",cen="PFS.event",
main="PFS BEP by treatment, by KRAS mutation",
trt="Arm", var="KRAS.mutant",
col=c("orange","orange","brown","brown"),
lty=c(3,1,3,1)))
## ----include=TRUE,fig.width=7, fig.height=7------------------------------
print(PlotKM(data=sample.data, tte="PFS",cen="PFS.event",
main="PFS BEP by treatment, by KRAS expression",
trt="Arm", var="KRAS.exprs", var.class="numeric",
percentile.cutoff=0.5,xlim=c(0,18))
)
## ----include=TRUE,fig.width=7, fig.height=7------------------------------
print(PlotKM(data=sample.data, tte="PFS",cen="PFS.event",
main="PFS BEP by treatment, by KRAS expression",
trt="Arm", var="KRAS.exprs", var.class="numeric",
numerical.cutoff=100)
)
## ----include=TRUE,fig.width=7, fig.height=7------------------------------
print(PlotKM(data=sample.data, tte="PFS",cen="PFS.event",
main="PFS BEP by treatment, by KRAS expression",
trt="Arm", var="KRAS.exprs", var.class="numeric",
numerical.cutoff=100, equal.in.high = F)
)
## ----include=TRUE,fig.width=7, fig.height=7------------------------------
print(PlotKM(data=sample.data, tte="PFS",cen="PFS.event",
main="PFS BEP by treatment, by KRAS expression",
trt="Arm", var="KRAS.exprs", var.class="numeric",
numerical.cutoff=c(100,500), xlim=c(0, 20))
)
## ----include=TRUE,fig.width=7, fig.height=7------------------------------
print(PlotKM(data=sample.data, tte="PFS",cen="PFS.event",
main="PFS BEP by treatment, by KRAS expression",
trt="Arm", var="KRAS.exprs", var.class="numeric",
numerical.cutoff=c(100,500),
col=c("green","green","green","brown","brown","brown"),
xlim=c(0,20))
)
## ----include=TRUE,fig.width=7, fig.height=7------------------------------
print(PlotKM(data=sample.data, tte="OS",cen="OS.event",
main="OS BEP by treatment, by KRAS mutation",
varlist=c("Arm","KRAS.mutant"),
varlist.levels=list(c("TRT","CTRL"),c("Wild Type","Mutant")),
legend.loc="left"))
## ----include=TRUE,fig.width=7, fig.height=7------------------------------
print(PlotKM(data=sample.data, tte="OS",cen="OS.event", bep="BEP",
main="OS BEP by treatment, by KRAS mutation", varlist=c("Arm","KRAS.mutant"),
varlist.levels=list(c("TRT","CTRL"),c("Wild Type","Mutant")),
varlist.labels=list(c("trt","ctrl"),c("wt","mut")),
plot.median=T,legend.loc="left"))
## ----include=TRUE,fig.width=7, fig.height=7------------------------------
print(PlotKM(data=sample.data, tte="PFS",cen="PFS.event",
var=c("Arm","KRAS.mutant"),
bep="BEP", legend.loc=NULL, legend.x=5, legend.y=.8))
## ---- fig.height=5,fig.width=7-------------------------------------------
PlotTabForestBiomarker(data=input,
outcome.class="survival",
outcome.var=c("PFS","PFS.event"),
trt="Arm",
var="KRAS.mutant",
var.class="categorical")
## ---- fig.height=10,fig.width=9------------------------------------------
PlotTabForestBiomarker(data=input,
outcome.class="survival",
outcome.var=c("PFS","PFS.event"),
trt="Arm",
var="KRAS.mutant",
var.class="categorical",
tabforest = TRUE)
## ---- fig.height=5,fig.width=7-------------------------------------------
PlotTabForestBiomarker(data=input,
outcome.class="survival",
outcome.var=c("PFS","PFS.event"),
trt="Arm",
var="KRAS.mutant",
var.class="categorical",
bep = 'BEP',
bep.indicator=1)
## ---- fig.height=4,fig.width=6-------------------------------------------
PlotTabForestBiomarker(data=input,
outcome.class="survival",
outcome.var=c("PFS","PFS.event"),
trt="Arm",
var="KRAS.mutant",
var.class="categorical",
var.name="KRAS mut",
show.itt=FALSE,
show.bep=FALSE)
## ---- fig.height=6,fig.width=9-------------------------------------------
PlotTabForestBiomarker(data=input,
outcome.class="survival",
outcome.var=c("PFS","PFS.event"),
trt="Arm",
var="KRAS.exprs",
var.class="numeric", var.name="KRAS exprs",
percentile.cutoff=c(.25,.5,.75),
# cols=c("black","black","darkgreen","darkgreen","darkgreen"),
numerical.cutoff=NULL,
greater=TRUE, less=FALSE,
within.bin=FALSE,
show.itt=TRUE, show.bep=TRUE)
## ---- fig.height=6,fig.width=9-------------------------------------------
PlotTabForestBiomarker(data=input,
outcome.class="survival",
outcome.var=c("PFS","PFS.event"),
trt="Arm",
var="KRAS.exprs",
var.class="numeric", var.name="KRAS exprs",
percentile.cutoff=c(.25,.5,.75),
numerical.cutoff=NULL,
greater=FALSE, less=TRUE,
within.bin=FALSE,
show.itt=TRUE, show.bep=TRUE,
bep = 'BEP', bep.indicator=1)
## ---- fig.height=6,fig.width=9-------------------------------------------
PlotTabForestBiomarker(data=input,
outcome.class="survival",
outcome.var=c("PFS","PFS.event"),
trt="Arm",
var="KRAS.exprs",
var.class="numeric", var.name="KRAS exprs",
percentile.cutoff=c(.25,.5,.75),
numerical.cutoff=NULL,
greater=TRUE, less=TRUE,
within.bin=FALSE,
show.itt=TRUE, show.bep=TRUE)
## ---- fig.height=6,fig.width=9-------------------------------------------
PlotTabForestBiomarker(data=input,
outcome.class="survival",
outcome.var=c("PFS","PFS.event"),
trt="Arm",
var="KRAS.exprs",
var.class="numeric", var.name="KRAS exprs",
percentile.cutoff=c(.25,.5,.75),
numerical.cutoff=NULL,
greater=TRUE, less=TRUE, greater.by.less = TRUE,
within.bin=FALSE,
show.itt=TRUE, show.bep=TRUE)
## ---- fig.height=6,fig.width=9-------------------------------------------
PlotTabForestBiomarker(data=input,
outcome.class="survival",
outcome.var=c("PFS","PFS.event"),
trt="Arm",
var="KRAS.exprs",
var.class="numeric", var.name="KRAS exprs",
percentile.cutoff=c(.25,.5,.75),
numerical.cutoff=NULL,
greater=FALSE, less=FALSE,
within.bin=TRUE,
show.itt=TRUE, show.bep=TRUE)
## ---- fig.height=6,fig.width=9-------------------------------------------
PlotTabForestBiomarker(data=input,
outcome.class="survival",
outcome.var=c("PFS","PFS.event"),
trt="Arm",
var="KRAS.exprs",
var.class="numeric", var.name="KRAS exprs",
percentile.cutoff=NULL,
numerical.cutoff=c(50,100),
greater=TRUE, less=FALSE,
within.bin=FALSE,
show.itt=TRUE, show.bep=TRUE)
## ---- fig.height=6,fig.width=9-------------------------------------------
PlotTabForestBiomarker(data=input,
outcome.class="survival",
outcome.var=c("PFS","PFS.event"),
trt="Arm",
var="KRAS.exprs",
var.class="numeric", var.name="KRAS exprs",
percentile.cutoff=NULL,
numerical.cutoff=c(50,100),
greater=TRUE, less=FALSE,
within.bin=FALSE,
show.itt=TRUE, show.bep=TRUE,
bep = 'BEP', bep.indicator=1, covariate="Age")
## ---- fig.height=6,fig.width=9-------------------------------------------
PlotTabForestBiomarker(data=input,
outcome.class="survival",
outcome.var=c("PFS","PFS.event"),
trt="Arm",
var="KRAS.exprs",
var.class="numeric", var.name="KRAS exprs",
percentile.cutoff=NULL,
numerical.cutoff=c(50,100),
greater=TRUE, less=FALSE,
within.bin=FALSE,
show.itt=TRUE, show.bep=TRUE,
bep = 'BEP', bep.indicator=1, strata="Sex")
## ---- fig.height=6,fig.width=9-------------------------------------------
PlotTabForestBiomarker(data=input,
outcome.class="survival",
outcome.var=c("PFS","PFS.event"),
trt="Arm",
var="KRAS.exprs",
var.class="numeric", var.name="KRAS exprs",
percentile.cutoff=NULL,
numerical.cutoff=c(50,100),
greater=TRUE, less=FALSE,
within.bin=FALSE,
show.itt=TRUE, show.bep=TRUE,
bep = 'BEP', bep.indicator=1,covariate="Age",strata="Sex")
## ---- fig.height=4,fig.width=6-------------------------------------------
PlotTabForestBiomarker(data=subset(input, Arm=="TRT"),
outcome.class="survival",
outcome.var=c("PFS","PFS.event"),
trt=NULL,
var="KRAS.exprs",
var.class="numeric", var.name="KRAS exprs",
percentile.cutoff=NULL,
numerical.cutoff=c(50,100),
greater=TRUE, less=FALSE,
within.bin=FALSE,
show.itt=TRUE, show.bep=TRUE,covariate="Age",strata="Sex")
## ---- fig.height=6,fig.width=9-------------------------------------------
PlotTabForestBiomarker(data=input,
outcome.class="survival",
outcome.var=c("PFS","PFS.event"),
trt="Arm",
var="KRAS.exprs",
var.class="numeric", var.name="KRAS exprs",
percentile.cutoff=c(.25,.5,.75),
numerical.cutoff=NULL,
greater=TRUE, less=FALSE,
within.bin=FALSE,
show.itt=TRUE, show.bep=TRUE,
covariate=NULL, #Sex
strata=NULL, #Age
placebo.code='TRT',
active.code='CTRL')
## ---- fig.height=12,fig.width=9------------------------------------------
PlotTabForestBiomarker(data=input,
outcome.class="survival",
outcome.var=c("PFS","PFS.event"),
trt="Arm",
var="KRAS.exprs",
var.class="numeric", var.name="KRAS exprs",
percentile.cutoff=c(.25,.5,.75),
numerical.cutoff=NULL,
greater=TRUE, less=FALSE,
within.bin=FALSE,
show.itt=TRUE, show.bep=TRUE,
across.and.within = TRUE)
## ---- fig.height=5,fig.width=7-------------------------------------------
PlotTabForestBiomarker(data=input,
outcome.class="binary",
outcome.var=c("Response"),
rsp.cat = TRUE,
rsp.response = c("CR","PR"),
rsp.nonresponse = c("SD", "PD","NON CR/PD","NE",NA),
trt="Arm",
var="KRAS.mutant",
var.class="categorical")
## ---- fig.height=10,fig.width=9------------------------------------------
PlotTabForestBiomarker(data=input,
outcome.class="binary",
outcome.var=c("Response"),
rsp.cat = TRUE,
rsp.response = c("CR","PR"),
rsp.nonresponse = c("SD", "PD","NON CR/PD","NE",NA),
trt="Arm",
var="KRAS.mutant",
var.class="categorical",
tabforest = TRUE)
## ---- fig.height=5,fig.width=7-------------------------------------------
PlotTabForestBiomarker(data=input,
outcome.class="continuous",
outcome.var=c("Lab_ontrt"),
trt="Arm",
var="KRAS.mutant",
var.class="categorical")
## ---- fig.height=10,fig.width=10-----------------------------------------
PlotTabForestBiomarker(data=input,
outcome.class="continuous",
outcome.var=c("Lab_ontrt"),
trt="Arm",
var="KRAS.mutant",
var.class="categorical",tabforest=T)
## ---- fig.height=12,fig.width=9------------------------------------------
PlotTabForestMulti(data=input,
outcome.class="survival",
outcome.var=c("PFS","PFS.event"),
trt="Arm",
var=c("Sex","Age"),
bep="BEP",bep.indicator=1,
compare.bep.itt=TRUE
)
## ---- fig.height=6,fig.width=9-------------------------------------------
PlotTabForestMulti(data=input,
outcome.class="survival",
outcome.var=c("PFS","PFS.event"),
trt="Arm",
var=c("Sex","Age"),
bep="BEP",bep.indicator=1, compare.bep.itt=FALSE,
compare.subgroup=TRUE, subgroup="KRAS.mutant"
)
## ---- fig.height=6,fig.width=9-------------------------------------------
PlotTabForestMulti(data=input,
outcome.class="survival",
outcome.var=c("PFS","PFS.event"),
trt="Arm",
var=c("Sex","Age"),
bep="BEP",bep.indicator=1, compare.bep.itt=FALSE,
compare.subgroup=TRUE, subgroup="KRAS.mutant", show.itt=TRUE
)
## ---- fig.height=12,fig.width=9------------------------------------------
PlotTabForestMulti(data=input,
outcome.class="survival",
outcome.var=c("PFS","PFS.event"),
trt="Arm",
var=c("Sex","Age"),
bep="BEP",bep.indicator=1, compare.bep.itt=FALSE,
compare.subgroup=TRUE, subgroup="KRAS.mutant", show.itt=TRUE, show.bep=TRUE
)
## ---- fig.height=12,fig.width=9------------------------------------------
PlotTabForestMulti(data=input,
outcome.class="survival",
outcome.var=c("PFS","PFS.event"),
trt="Arm",
var=c("Sex","Age"), compare.bep.itt=FALSE,
compare.subgroup=TRUE, subgroup="KRAS.mutant", show.itt=TRUE, show.bep=TRUE
)
## ---- fig.height=6,fig.width=9-------------------------------------------
PlotTabForestMulti(data=subset(input,Arm=="TRT"),
outcome.class="survival",
outcome.var=c("PFS","PFS.event"),
trt=NULL,
var=c("Sex","Age"),
bep="BEP",bep.indicator=1, compare.bep.itt=TRUE
)
## ---- fig.height=12,fig.width=9------------------------------------------
PlotTabForestMulti(data=input,
outcome.class="survival",
outcome.var=c("PFS","PFS.event"),
trt="Arm", percentile.cutoff=c(.33,.66),
var=c("Sex","Age"),
bep="BEP",bep.indicator=1, compare.bep.itt=FALSE,
compare.subgroup=TRUE, subgroup="KRAS.mutant"
)
## ---- fig.height=12,fig.width=9------------------------------------------
PlotTabForestMulti(data=input,
outcome.class="survival",
outcome.var=c("PFS","PFS.event"),
trt="Arm", percentile.cutoff=c(.33,.66),less=TRUE,greater=FALSE,
var=c("Sex","Age"),
bep="BEP",bep.indicator=1, compare.bep.itt=FALSE,
compare.subgroup=TRUE, subgroup="KRAS.mutant"
)
## ---- fig.height=8,fig.width=9-------------------------------------------
PlotTabForestMulti(data=input,
outcome.class="survival",
outcome.var=c("PFS","PFS.event"),
trt="Arm", percentile.cutoff=c(.33,.66),within.bin=TRUE,
var=c("Sex","Age"),
bep="BEP",bep.indicator=1, compare.bep.itt=FALSE,
compare.subgroup=TRUE, subgroup="KRAS.mutant"
)
## ---- fig.height=6,fig.width=9-------------------------------------------
PlotTabForestMulti(data=input,
outcome.class="survival",
outcome.var=c("PFS","PFS.event"),
trt="Arm",
var=c("Sex","Age"),
compare.bep.itt=FALSE, compare.subgroup=FALSE,itt.name=""
)
## ---- fig.height=6,fig.width=9-------------------------------------------
PlotTabForestMulti(data=input,
outcome.class="binary",
outcome.var=c("Response"),
rsp.cat = TRUE,
rsp.response = c("CR","PR"),
rsp.nonresponse = c("SD", "PD","NON CR/PD","NE",NA),
trt="Arm",
var=c("Sex","Age"),
compare.bep.itt=FALSE, compare.subgroup=FALSE,itt.name=""
)
## ---- fig.height=10,fig.width=10-----------------------------------------
PlotTabForestMulti(data=input,
outcome.class="binary",
outcome.var=c("Response"),
rsp.cat = TRUE,
rsp.response = c("CR","PR"),
rsp.nonresponse = c("SD", "PD","NON CR/PD","NE",NA),
trt="Arm",
var=c("Sex","Age"),
compare.bep.itt=FALSE, compare.subgroup=FALSE,itt.name="", tabforest=T
)
## ---- fig.height=6,fig.width=9-------------------------------------------
PlotTabForestMulti(data=input,
outcome.class="continuous",
outcome.var=c("Lab_ontrt"),
trt="Arm",
var=c("Sex","Age"),
compare.bep.itt=FALSE, compare.subgroup=FALSE,itt.name=""
)
## ---- fig.height=10,fig.width=10-----------------------------------------
PlotTabForestMulti(data=input,
outcome.class="continuous",
outcome.var=c("Lab_ontrt"),
trt="Arm",
var=c("Sex","Age"),
compare.bep.itt=FALSE, compare.subgroup=FALSE,itt.name="", tabforest=T
)
## ------------------------------------------------------------------------
PlotSTEPP(data = input,
outcome.var = c("PFS", "PFS.event"),
outcome.class = "survival",
trt = "Arm",
var = "KRAS.exprs",
placebo.code = "CTRL",
active.code = "TRT",
csv.name = NULL,
pdf.name = NULL
)
## ------------------------------------------------------------------------
PlotSTEPP(data = input,
outcome.var = "Baseline.SLD",
outcome.class = "continuous",
trt = "Arm",
var = "KRAS.exprs",
covariate= "Sex",
placebo.code = "CTRL",
active.code = "TRT",
csv.name = NULL,
pdf.name = NULL
)
## ------------------------------------------------------------------------
PlotSTEPP(data = input,
outcome.var = "ECOG",
outcome.class = "binary",
trt = "Arm",
var = "KRAS.exprs",
placebo.code = "CTRL",
active.code = "TRT",
csv.name = NULL,
pdf.name = NULL
)
## ------------------------------------------------------------------------
CoxTab(data=sample.data, tte="OS", cens="OS.event",bep='BEP', var='Sex' )
## ------------------------------------------------------------------------
kable(
CoxTab(data=sample.data,tte="OS", cens="OS.event", var=c('Sex',"Country","Age"),
var.class=c("categorical","categorical","numeric"))
)
## ------------------------------------------------------------------------
kable(
CoxTab(data=sample.data,tte="OS", cens="OS.event", var=c('Sex',"Country","Age"))
)
## ------------------------------------------------------------------------
kable(
CoxTab(data=sample.data,tte="OS", cens="OS.event", var=c('Sex',"Country","Age"),
var.class=c("categorical","categorical","numeric"), bep="BEP")
)
## ------------------------------------------------------------------------
kable(
CoxTab(data=sample.data,tte="OS", cens="OS.event", var=c('Sex',"Country","Age"),
var.class=c("ordered.factor","categorical","numeric"),
ordered.factor.levels.list=list(Sex=c("M","F")),bep="BEP")
)
## ------------------------------------------------------------------------
kable(
CoxTab(data=sample.data,tte="OS", cens="OS.event", var=c('Sex',"Country","Age"),
additive=FALSE)
)
## ------------------------------------------------------------------------
SummaryTwoGroups(outcome.var = input$OS, treatment.var = input$Arm,
placebo.code = "CTRL", active.code = "TRT",
outcome.class = "continuous")
## ------------------------------------------------------------------------
SummaryTwoGroups(outcome.var = input$OS, treatment.var = input$Arm,
placebo.code = "CTRL", active.code = "TRT",
outcome.class = "continuous", covariate.var = input$Sex)
## ------------------------------------------------------------------------
SummaryTwoGroups(outcome.var = input$OS, treatment.var = input$Arm,
placebo.code = "CTRL", active.code = "TRT",
outcome.class = "continuous", covariate.var = input$Sex,
return.fit = TRUE)
## ------------------------------------------------------------------------
SummaryTwoGroups(outcome.var = input$OS.event, treatment.var = input$Arm,
placebo.code = "CTRL", active.code = "TRT",
outcome.class = "binary")
## ------------------------------------------------------------------------
SummaryTwoGroups(outcome.var = input[, c("OS", "OS.event")],
treatment.var = input$Arm, placebo.code = "CTRL",
active.code = "TRT", outcome.class = "survival")
## ------------------------------------------------------------------------
SummaryTwoGroups(outcome.var = input[, c("OS", "OS.event")],
treatment.var = input$Arm, placebo.code = "CTRL",
active.code = "TRT", outcome.class = "survival",
covariate.var = input$Sex)
## ------------------------------------------------------------------------
SummaryTwoGroups(outcome.var = input[, c("OS", "OS.event")],
treatment.var = input$Arm, placebo.code = "CTRL",
active.code = "TRT", outcome.class = "survival",
covariate.var = input$Sex, strat.factor.var = input$Age)
## ------------------------------------------------------------------------
kable(
LogRankTab(data=input,tte="PFS",cens="PFS.event",var="Arm")
)
## ------------------------------------------------------------------------
example <- data.frame( y=c(rnorm(30)+10, rnorm(4)+20, rnorm(15)+15, NA),
time=c(rep("t2", 30), rep("t4",4), rep("t1", 15), "t3"),
grp=sample(1:3, 50, TRUE), sex=sample(1:2, 50, TRUE))
head(example)
str(example)
## ----include=TRUE,fig.width=7, fig.height=4------------------------------
BoxPlot(list(a=rnorm(50,,3), b=rnorm(25,1,4), c=rnorm(75,2,1)))
## ----include=TRUE,fig.width=7, fig.height=4------------------------------
BoxPlot(list(a=rnorm(50,,3), b=rnorm(25,1,4), c=rnorm(75,2,1)), horizontal=TRUE,
Xaxis=list(las=2, hadj=2), Xaxis2=list(las=2, hadj=-.25))
## ----include=TRUE,fig.width=7, fig.height=4------------------------------
BoxPlot(matrix(rnorm(100), ncol=4, dimnames=list(NULL, LETTERS[1:4])) )
## ----include=TRUE,fig.width=7, fig.height=4------------------------------
BoxPlot(rnorm(50,,3), rnorm(25,1,2), rnorm(75,2,1))
## ----include=TRUE,fig.width=7, fig.height=4------------------------------
BoxPlot(rnorm(50,,3), rnorm(25,1,2), rnorm(75,2,1), horizontal=TRUE)
## ----include=TRUE,fig.width=7, fig.height=4------------------------------
BoxPlot(example, y~time, sc.pch=16)
## ----include=TRUE,fig.width=7, fig.height=4------------------------------
BoxPlot(example, y~time, sc.pch=16, box.type="bp")
## ----include=TRUE,fig.width=7, fig.height=4------------------------------
BoxPlot(example, y~time, sc.pch=16, box.type="bp", Title=list(main="Custom Main Title"))
## ----include=TRUE,fig.width=7, fig.height=4------------------------------
BoxPlot(example, y~time, trend="median", ylab="Y-Axis Label")
## ----include=TRUE,fig.width=7, fig.height=4------------------------------
BoxPlot(example, y~time, trend="median", ylab="Y-Axis Label",
sc.col=c("red", "blue", "green")[example$grp] )
## ----include=TRUE,fig.width=7, fig.height=4------------------------------
BoxPlot(example, y~time, trend="median", ylab="Y-Axis Label",
sc.col=c("red", "blue", "green")[example$grp],
sc.pch=c(5,10)[example$sex] )
legend("bottomright", fill=c("red", "green", "blue", "white", "white"),
legend=c("Stage I", "Stage II", "Stage III", "Female", "Male"),
pch=c(-1, -1, -1, 5, 10), border=NA)
## ----include=TRUE,fig.width=7, fig.height=4------------------------------
example2 <- data.frame(y1=12+rnorm(15), y2=15+rnorm(15), y3=25+rnorm(15))
## ----include=TRUE,fig.width=7, fig.height=4------------------------------
BoxPlot(example2, var=c("y1", "y2", "y3"), Grid=TRUE, trend="mean")
## ----include=TRUE,fig.width=7, fig.height=4------------------------------
BoxPlot(example2, var=c("y1", "y2", "y3"), box.type="bp", Grid=TRUE)
## ----include=TRUE,fig.width=7, fig.height=4------------------------------
BoxPlot(rnorm(1856, 5), runif(1245, 2,10), exp(rnorm(2311)), sc.col=as.rgb("black", .05),
box.type="bp", Xaxis=list(labels=c("~N(5,1)", "~Unif(2,10)", "~exp(N(0,1))")), ylim=c(0,15))
## ----include=TRUE,fig.width=7, fig.height=4------------------------------
mat <- matrix(c(rep(10,45), rep(15,45), rep(35,45))+rnorm(135), ncol=3)
BoxPlot(mat, trend="mean", trend.col="red", Ylabel=list(text="Example Measurements"))
## ----include=TRUE,fig.width=7, fig.height=4------------------------------
data(mtcars)
BoxPlot(mtcars, mpg~gear:cyl)
## ----include=TRUE,fig.width=7, fig.height=4------------------------------
BoxPlot(mtcars, mpg~cyl %in% gear)
## ----include=TRUE,fig.width=7, fig.height=4------------------------------
dat <- mtcars
dat$cyl <- factor(dat$cyl, levels=c(4,6,8), labels=c("4Cyl", "6Cyl", "8Cyl"))
dat$gear <- factor(dat$gear, levels=c(3,4,5), labels=c("3Gear", "4Gear", "5Gear"))
BoxPlot(dat, mpg~cyl %in% gear)
## ----include=TRUE,fig.width=7, fig.height=4------------------------------
BoxPlot(dat, mpg~cyl:gear, XaxisTab=list(),mar=c(8,3,5,1))
## ----include=TRUE,fig.width=7, fig.height=4------------------------------
BoxPlot(mtcars, mpg~cyl:gear, XaxisTab=list(), mar=c(5,8,5,4),
horizontal=TRUE, Ylabel=list(text="Y-axis label now appearing on X-axis"))
## ----include=TRUE,fig.width=7, fig.height=4------------------------------
BoxPlot(dat, mpg~cyl:gear, XaxisTab=list(font=2, col="darkblue", cex=1.25), mar=c(5,3,5,1))
## ----include=TRUE,fig.width=7, fig.height=4------------------------------
BoxPlot(dat, mpg~cyl:gear, XaxisTab=list(Label=list(font=2, col="darkblue", cex=1.25),
Text=list(col="red")), mar=c(5,3,5,1))
## ----include=TRUE,fig.width=7, fig.height=4------------------------------
BoxPlot(dat, mpg~cyl:gear:vs, XaxisTab=list(), mar=c(5,3,5,1))
## ----include=TRUE,fig.width=7, fig.height=4------------------------------
BoxPlot(mtcars, mpg~cyl %in% gear,
Xaxis=list(labels=paste(rep(c("4Cyl", "6Cyl", "8Cyl"),3),
c(rep("3Gear",3), rep("4Gear",3), rep("5Gear",3)), sep=".")))
## ----include=TRUE,fig.width=7, fig.height=4------------------------------
BoxPlot(dat, mpg~cyl %in% gear, Title=list(main="Miles per Gallon by Number of Gears",
col.main="Green", cex.main=2.5), vline=c(3.5, 6.5), vl.lty=2, vl.col="gray", vl.lwd=2,
Xaxis=list(labels=NA, at=1:9, tick=TRUE), col=c(rep("blue", 3), rep("red", 3), rep("green", 3)),
Xaxis2=list(tick=FALSE), Yaxis=list(at=seq(10,34,2)), Grid=list(x=1:9, y=seq(10,34,2)),
Xlabel=list(text=paste(rep(c("4Cyl", "6Cyl", "8Cyl"),3), c(rep("3Gear",3), rep("4Gear",3), rep("5Gear",3))),
at=1:9, las=2, adj=1, line=0.75, col=c(rep("blue", 3), rep("red", 3), rep("green", 3))),
mean.col=c(rep("cyan", 3), rep("orange", 3), rep("magenta", 3)), Box=FALSE, trend="mean",mar=c(6,4,5,2) )
## ----include=TRUE,fig.width=7, fig.height=4------------------------------
BoxPlot(mtcars, mpg~cyl %in% gear, Title=list(main="Miles per Gallon by Number of Gears", col.main="#84d52b", cex.main=1.5),
vline=c(3.5, 6.5), vl.lty=2, vl.col="gray", vl.lwd=2,
Xaxis2=list(tick=FALSE, las=2, hadj=-.25), Yaxis=list(at=seq(10,34,2)), Grid=list(x=1:9, y=seq(10,34,2)),
mean.col=c(rep("cyan", 3), rep("orange", 3), rep("magenta", 3)), Box=FALSE, trend="mean",
mar=c(3, 7, 4, 4), horizontal=TRUE, sc.pch=c(0, 15)[dat$am+1], sc.col="wheat4",
XaxisTab=list(Text=list(col=c(rep("cyan", 3), rep("orange", 3), rep("magenta", 3)))) )
legend(x="topright", pch=c(0, 15), legend=c("automatic", "manual"), box.lty=0, col="wheat4")
## ------------------------------------------------------------------------
PlotLong(longbmkr, aes(x=vm, y=ep),
xlab = 'Visitation Month',
ylab = 'Biomarker Endpoint',
labs.title = 'Mean +/- SEM')
## ------------------------------------------------------------------------
PlotLong(longbmkr, aes(x=vm, y=ep), fun.data = 'tukey',
xlab = 'Visitation Month',
ylab = 'Biomarker Endpoint',
labs.title = 'Tukey Whiskers and Hinges')
## ------------------------------------------------------------------------
PlotLong(longbmkr, aes(x=vm, y=ep, group=trt, color=trt, fill=trt),
fun.data = 'tukey', facet.fun = . ~ sex,
xlab = 'Visitation Month',
ylab = 'Biomarker Endpoint',
labs.title = 'Biomarker Timecourse',
labs.caption = 'Ribbons represent Tukey hinges and whiskers')
## ---- fig.height = 3.5,eval=TRUE-----------------------------------------
library(dplyr)
PlotLong(longbmkr %>% filter(vm <= 24),
aes(x=vm, y=ep, group=trt, color=trt, fill=trt),
fun.data = 'tukey', facet.fun = . ~ sex,
show.counts = 'table',
xlab = 'Visitation Month',
ylab = 'Biomarker Endpoint',
labs.title = 'Biomarker Timecourse',
labs.caption = 'Ribbons represent Tukey hinges and whiskers')
## ---- fig.height = 3.5, eval=TRUE----------------------------------------
PlotLong(longbmkr %>% filter(vm <= 24),
aes(x=vm, y=ep, group=trt, color=trt, fill=trt),
fun.data = 'tukey', facet.fun = . ~ sex,
show.counts = 'table',
plot.style = 'errorbars',
xlab = 'Visitation Month',
ylab = 'Biomarker Endpoint',
labs.title = 'Biomarker Timecourse',
labs.caption = 'Ribbons represent Tukey hinges and whiskers')
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.