ToxPlot_byCycle: Summary plot of toxicities by cycle
In csmoxford/robustToxicities: Toxicity tables

Description Usage Arguments See Also Examples

This plot summarises the proportion of patients having an adverse event in each time period as defined by periodDividerCols in the robustToxicitiesClass.

1 2	ToxPlot_byCycle(rt, gradeRequired = 1, col = c("blue", "red"), tableSpace = 0.1, las = 1, legendPosition = "right", add = FALSE)

`rt`	An object of class robustToxicities
`gradeRequired`	Only include adverse events with at least this grade
`col`	A vector of colours to plot each arm with
`tableSpace`	A parameter to assist in vertical row spacing the table appropriately
`las`	numeric in 0,1,2,3; the style of axis labels. 0: always parallel to the axis, 1: always horizontal [default], 2: always perpendicular to the axis, 3: always vertical
`legendPosition`	The location to place the legend see `legend` for details
`add`	TRUE/FALSE whether to add to an existing plot or start a new one

ToxPlot_byPatient, ToxPlot_byToxicity, ToxPlot_byTime

# 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)

##########################################################
par(mar = c(4,6,3,2))
ToxPlot_byCycle(rt)

##########################################################
# subset to a specific set of adverse events
rt@toxData$ass_TRUE = rt@toxData$toxicity == "Sore Throat"
par(mar = c(4,6,3,2))
ToxPlot_byCycle(rt)