Step 5: Visualise temporal symmetry

Introduction

In this vignette we will explore the functionality and arguments of a set of functions that will help us to understand and visualise the temporal symmetry results (produced Step 4: Obtain aggregated data on temporal symmetry). In particular, we will delve into the following function:

  • plotTemporalSymmetry(): to plot the temporal symmetry.

This function builds-up on previous functions, such as generateSequenceCohortSet() and summariseTemporalSymmetry() function.

Let’s regather the output from summariseTemporalSymmetry()

temporal_symmetry <- summariseTemporalSymmetry(cohort = cdm$intersect)

With this established, much like summariseSequenceRatios(), the object temporal_symmetry could then be fed into summariseTemporalSymmetry() to visualise the results:

plotTemporalSymmetry(result = temporal_symmetry)

Note that the x axis is the time, which we recall to be the initiation of the marker minus the initiation of the index. The unit of the time difference here is month as this is the default from summarisTemporalSymmetry().

Modify xlim and labs

If one changes the timescale for summarisTemporalSymmetry() to be day then logically one should change the xlim and labs accordingly like so:

temporal_symmetry_day <- summariseTemporalSymmetry(cohort = cdm$intersect, timescale = "day")

plotTemporalSymmetry(result = temporal_symmetry_day,
                     labs = c("Time (days)", "Individuals (N)"),
                     xlim = c(-365, 365))

Modify plotTitle

Much like what we already saw in Step 3. Visualise the sequence ratios. One could do the following:

plotTemporalSymmetry(result = temporal_symmetry,
                     plotTitle = "Plot Temporal Symmetry")

Modify colours

colours could be modified like so (remember two colours are required):

plotTemporalSymmetry(result = temporal_symmetry,
                     colours = c("orange", "purple"))

Modify scales

The scale parameter is designed for the users to have a choice as to whether to set free y scales for the facet wrap when there are multiple plots (i.e. each plot has its own scaled y axis) or set them equal for all. Only accepts “free” for the former and “fixed” for the latter.

For the cdm$intersect we have, it does not make a difference setting it to “fixed” or “free” (default). However, should one wish to set it to “fixed”, one should do:

plotTemporalSymmetry(result = temporal_symmetry,
                     scales = "fixed")
CDMConnector::cdmDisconnect(cdm = cdm)

That would be the end of the vignette, have fun with the package!