plotTS: Plotting Time-Series Data

In DHLab-TSENG/lab: a package for EHR laboratory data

Plotting Time-Series Data

Description

plotTimeSeriesLab plots line charts of laboratory data.

Usage

plotTimeSeriesLab(
  labData,
  idColName,
  labItemColName,
  timeMarkColName,
  valueColName,
  timeStart = NULL,
  timeEnd = NULL,
  abnormalMarkColName = NULL
)

Arguments

labData	a file or dataframe of laboratory test data with at least 4 columns about patient ID, lab item, test value and test date, respectively.
idColName	the column name that records patient ID in labData.
labItemColName	the column name that records lab item in labData. If lab code is combined by multiple columns, then just simply add + operator between column names, e.g., A + B.
timeMarkColName	the column name that records time in labData. Time can be time window or be real date.
timeStart	any starting time point of interesting. It can be time window or be real date depending on the selection of timeMarkColName.
timeEnd	any ending time point of interesting. It can be time window or be real date depending on the selection of timeMarkColName.
abnormalMarkColName	the column name that records abnormal mark in labData. It is optional.

Details

This function provides an overview and temporal changes of laboratory tests. If abnormalMarkColName provided, then "H" mark is displayed by "▲" icon. Similarly, "L" mark is displayed by "▽" icon. Time mark can be continuous or discrete, but labData should be longitudinal.

Value

One or multiple line chart of temoral laboratory results of one or multiple patient(s).

Examples

timeSeriesData <- getTimeSeriesLab(labData = labSample,
                                   idColName = SUBJECT_ID,
                                   labItemColName = ITEMID,
                                   dateColName = CHARTTIME,
                                   valueColName = VALUENUM,
                                   indexDate = first,
                                   gapDate = 30,
                                   completeWindows = TRUE)
timeSeriesPlot <-plotTimeSeriesLab(labData = timeSeriesData,
                                   idColName = ID,
                                   labItemColName = ITEMID,
                                   timeMarkColName = Window,
                                   valueColName = Nearest,
                                   timeStart = 1,
                                   timeEnd  = 5,
                                   abnormalMarkColName = NULL)
plot(timeSeriesPlot)
# With abnormal mark
loincSample <- mapLOINC(labData = labSample,
                       labItemColName = ITEMID,
                       mappingTable = mapSample)
timeSeriesDataLOINC <- getTimeSeriesLab(labData = loincSample,
                                  idColName = SUBJECT_ID,
                                  labItemColName = LOINC + LABEL,
                                  dateColName = CHARTTIME,
                                  valueColName = VALUENUM,
                                  indexDate = first,
                                  gapDate = 30,
                                  completeWindows = TRUE)
colnames(patientSample)[2]<-"ID"
timeSeriesDataMarked <- getAbnormalMark(labData = timeSeriesDataLOINC,
                                       idColName = ID,
                                       labItemColName = LOINC,
                                       valueColName = Nearest,
                                       genderColName = GENDER,
                                       genderTable = patientSample,
                                       referenceTable = refLOINC)

timeSeriesPlotMarked <- plotTimeSeriesLab(labData = timeSeriesDataMarked,
                                         idColName = ID,
                                         labItemColName = LOINC + LABEL,
                                         timeMarkColName = Window,
                                         valueColName = Value,
                                         timeStart = 1,
                                         timeEnd = 5,
                                         abnormalMarkColName = ABMark)
plot(timeSeriesPlotMarked)

DHLab-TSENG/lab documentation built on Sept. 1, 2023, 9:03 p.m.