toxPlot_byToxicity: Plot toxicities over time
In csmoxford/robustToxicities: Toxicity tables

Description Usage Arguments Value See Also Examples

This function plots the worst grade of each toxicity over time. There should be no overlap between toxicities but in the case that there is the wors grade is given priority.

ToxPlot_byToxicity(rt, rowID_range = NULL, plotNow = TRUE,
  plotLeftSideOption = "treatment", xlim = c(-7, 60), xlab = character(0),
  plotCycleLength = 21, plotXLegendScale = "days", permitMarSet = TRUE,
  causality = NULL, events = list(), offsetEvent = NULL)

`rt`	an object of class robustToxicities
`rowID_range`	optional, a length 2 vector detailing the minimum and maximum row to plot
`plotNow`	whether to plot the graph or return the number of rows to plot
`plotLeftSideOption`	What to display on right axis. Options are: "treatment", "patid" or "both". Default is "treatment"
`xlim`	Range to plot on xaxis. Default is c(-7,60)
`xlab`	xaxis title / label
`plotCycleLength`	Cycle length is used to add greater highlights to vertical lines. Default is 21
`plotXLegendScale`	What scale to use on xaxis. Options are "days","weeks","months". Default is "days"
`permitMarSet`	Allow the function to set the mar for the plot
`causality`	Adds causality columns to the plot on the righthand side. This must be an object of type `causalityInfo-class`
`events`	a list of Objects of type eventInfo.
`offsetEvent`	the name of a column in patientData to use as time 0. If not provided the start of assessment date is used

This plot function return the number of row of unique toxicities * patients. This assists in computing optimal size for saved graphs.

ToxPlot_byPatient, ToxPlot_byTime, ToxPlot_byCycle

# Patient Level Data
data("rt_patientData")
# Toxicity Level Data
data("rt_toxicityData")


# Run the setup command passing in all the column names.
rt = SetupRobustToxicities(
  toxData = rt_toxicityData,
  patientData = rt_patientData,
  patidCol = "patientNo", treatmentCol = "Treatment",
  toxCategoryCol = "category", toxNameCol = "toxicity",
  toxGradeCol = "grade", dateOfStartOfToxWindow = "Registration_date",
  dateOfStartTox = "ae_onset_date", dateOfEndTox = "ae_resolve_date",
  dateOfEndOfToxWindow = "end_of_assessment_date",
  periodDividerCols = c("Registration_date", "Cycle_1_date","Cycle_2_date",
                        "Cycle_3_date", "Cycle_4_date", "Cycle_5_date", "Cycle_6_date"),
  periodDividerLabels = c("Pre treatment", "Cycle 1","Cycle 2",
                          "Cycle 3","Cycle 4","Cycle 5", "Cycle 6"),
  treatmentCodes = NULL, treatmentLabels = NULL, options = NULL)

# Look for queries. Note: must be called before running any
# of the functions on this class.
rt = QueryRobustToxicities(rt)

##########################################################
ToxPlot_byToxicity(rt)

##########################################################
# Subset to a range. Usefull for plotting over a number of figures if there
# are lots of adverse events
ToxPlot_byToxicity(rt, rowID_range = c(1,7))

##########################################################
# subset to a specific set of adverse events
rt@toxData$ass_TRUE = rt@toxData$Treatment == "Placebo"
ToxPlot_byToxicity(rt)

###########################################################
# Add causality data
rt@toxData$ass_TRUE = TRUE

# With causality
# Not provided so generate some for illustrative purposes
rt@toxData$causality1 = sample(1:5,28, replace = TRUE)
rt@toxData$causality2 = sample(1:5,28, replace = TRUE)

causality = ToxPlot_causalityInfo(
  columns = c("causality1","causality2"),
  names = c("A","B"),
  width = 1.5,
  cex = 1.2)

ToxPlot_byToxicity(rt,
                   causality = causality)


#########################################################
# Add event data

event_EOT = ToxPlot_eventInfo(
  columns = c("end_of_treatment_date"),
  label = c("End Of Treatment"),
  lwd = 4,
  col = c("blue")
)

event_EOA = ToxPlot_eventInfo(
  columns = c("end_of_assessment_date"),
  label = c("End Of Assessment"),
  lwd = 4,
  col = c("green")
)

ToxPlot_byToxicity(rt,
                   causality = causality,
                   xlim = c(-7, 100),
                   events = list(event_EOT, event_EOA))


########################################################
# Change offset

event_SOT = ToxPlot_eventInfo(
  columns = c("Registration_date"),
  label = c("Registration Date"),
  lwd = 4,
  col = c("orange")
)

ToxPlot_byToxicity(rt,
                   causality = causality,
                   xlim = c(-67, 40),
                   xlab = "Days from end of treatment",
                   events = list(event_SOT, event_EOT, event_EOA),
                   offsetEvent = "end_of_treatment_date")