Generate several plots to visualise TrackMate data and generate a report. The use of um is because ggsave does not currently save unicode to PDF reliably. The code is switchable to accommodate making a "report" (one dataset) or a "summary" (several related datasets combined)
Usage
makeSummaryReport(
tmList,
msdList,
jumpList,
tddf,
fddf,
titleStr = "",
subStr = "",
auto = FALSE,
summary = FALSE,
...
)Arguments
- tmList
list of trackmate data and calibration
- msdList
MSD summary and alpha list = output from calculateMSD()
- jumpList
list of a data frame of jump data and a variable to be passed to timeRes
- tddf
data frame of track density data
- fddf
data frame of fractal dimension data
- titleStr
string used as the title for the report
- subStr
string used as the subtitle for the report
- auto
boolean which selects for returning the patchwork report (FALSE) or a list of the patchwork report and a data frame of summary (TRUE)
- summary
boolean which selects for report (FALSE) or summary (TRUE)
- ...
additional arguments passed to methods
Examples
xmlPath <- system.file("extdata", "ExampleTrackMateData.xml", package="TrackMateR")
tmObj <- readTrackMateXML(XMLpath = xmlPath)
#> Units are: 1 pixel and 0.07002736 s
#> Spatial units are in pixels - consider transforming to real units
#> Extracting spot data...
#> Matching track data...
#> Calculating distances...
tmObj <- correctTrackMateData(tmObj, xyscalar = 0.04)
#> Correcting XY scale.
tmDF <- tmObj[[1]]
calibrationDF <- tmObj[[2]]
msdObj <- calculateMSD(df = tmDF, method = "ensemble", N = 3, short = 8)
jdObj <- calculateJD(dataList = tmObj, deltaT = 1)
tdDF <- calculateTrackDensity(dataList = tmObj, radius = 1.5)
fdDF <- calculateFD(dataList = tmObj)
fileName <- tools::file_path_sans_ext(basename(xmlPath))
reportObj <- makeSummaryReport(tmList = tmObj, msdList = msdObj, jumpList = jdObj,
tddf = tdDF, fddf = fdDF, titleStr = "Report", subStr = fileName, auto = TRUE)