Bubble Chart

BubbleChart visualizes baseline vs fold change in titers

BubbleChart(dat_list, subjectCol = "SubjectID", fit = NULL,
  yMinZero = FALSE, eqSize = 6/log2(length(dat_list) + 1), colorBy = NULL,
  xlimits = c(1.5, 10.5), xbreaks = 2:10, ylimits = c(-0.5, 10),
  ybreaks = seq(0, 10, 2), plot = TRUE, cols = 2, ...)

Arguments

dat_list	a named list like the one returned by FormatTiters. Values are assumed to be log2-transformed.
subjectCol	the name of the column specifying a subject ID. Default is "SubjectID".
fit	what type of fit to add. Current options are "lm" for linear model, "exp" for exponential, or NULL for no smoothing.
yMinZero	a logical specifying whether fitted y values below 0 should be set to 0.
eqSize	Text size of the equation. Only relevant if fit is not NULL
colorBy	a character string specifying an endpoint to colorBy or NULL (default) for no coloring.
xlimits	the x-axis limits (passed to scale_x_continuous)
xbreaks	the x-axis breaks (passed to scale_x_continuous)
ylimits	the y-axis limits (passed to scale_y_continuous)
ybreaks	the y-axis breaks (passed to scale_y_continuous)
plot	logical indicating whether to plot or not. Default is TRUE
cols	numeric specifying how many columns to layout plot
...	other arguments besides method and subjectCol passed to Calculate_maxRBA.

Value

(invisibly) a list of ggplot2 objects.

Details

This plot was designed for HAI titer data with baseline columns and fold change columns for multiple strains.

See also

FormatTiters

Examples

## Prepare the data
titer_list <- FormatTiters(Year2_Titers)
#> - Log transforming Pre and Post columns
#> - Setting any negative log fold changes to 0

## Basic plot without any fitted model
BubbleChart(titer_list)

## Change layout to plot all in a single column
BubbleChart(titer_list, cols = 1)

## Add a linear fit
BubbleChart(titer_list, fit = "lm")

## Add an exponential fit
BubbleChart(titer_list, fit = "exp")

## Add coloring by age
BubbleChart(titer_list, fit = "exp", colorBy = "AgeGroup")