Bubble Plot to Visualize Occurrences of NA gap sizes

Source: R/ggplot_na_gapsize2.R

Visualize the total NA count (gap size * occurrence) for the existing gaps sizes (NAs in a row).

ggplot_na_gapsize2(
  x,
  colors_bubbles = c("#FCFBFF", "#EFEEFA", "#DDDAEF", "#C8C3E2", "#B1AAD4", "#9A8FC4",
    "#8273B5", "#6B56A7", "#553695", "#3D1778"),
  color_border = "black",
  alpha_bubbles = 0.4,
  labels_bubbles = "none",
  size_bubbles = 25,
  min_totals = NULL,
  min_occurrence = NULL,
  min_gapsize = NULL,
  max_gapsize = NULL,
  title = "Gap Size Analysis",
  subtitle = "Total NA counts for different gapsizes",
  xlab = "Gapsize",
  ylab = "Number occurrence",
  legend = TRUE,
  legend_breaks = 4,
  legend_title = "Total NAs",
  legend_position = "right",
  legend_point_sizes = "default",
  theme = ggplot2::theme_linedraw()
)

Arguments

x

Numeric Vector (vector) or Time Series (ts) object containing NAs. This is the only mandatory parameter - all other parameters are only needed for adjusting the plot appearance.
colors_bubbles

Choose a color gradient that encodes lower to higher total NA counts. Color codes can be given as vector. Using color palettes from colorspace, grDevices, RColorBrewer or other packages is useful here. E.g. grDevices::heat.colors(10) would be a possible input.
color_border

Color for the border of the bubbles.
alpha_bubbles

Alpha (transparency) value used for filling the bubbles.
labels_bubbles

Should labels be added to the individual bubbles inside the plot. For many datasets there will be overplotting issues once labels are added. In these cases using the min_gapsize, min_totals or min_occurrence options might be useful to only display the most relevant gap sizes.

You can choose between these labels to be added:

  • "none" - No label gets added to the bubbles (default choice)

  • "gap" - Adds a label displaying the gap size belonging to the respective bubble

  • "total" - Adds a label displaying the total NA count for the respective bubble

  • "gap-occurrence" - Adds a label displaying the respective gap size and number of its occurrence

The default setting is "none".
size_bubbles

Allows to scale the size of the bubbles. Some experimenting with this parameter might be needed to get a good visualization for your specific dataset.
min_totals

Only print bubbles for gap sizes that account for at least min_totals NAs in the time series.
min_occurrence

Only print bubbles for gap sizes that occur at least min_occurrence times in the time series.
min_gapsize

Only show gap sizes larger than min_gapsize. Together with max_gapsize enables zooming into in certain regions of interest.
max_gapsize

Only show gapsizes smaller than max_gapsize. Together with min_gapsize enables zooming into in certain regions of interest.
title

Title of the Plot.
subtitle

Subtitle of the Plot.
xlab

Label for x-Axis.
ylab

Label for y-Axis.
legend

If TRUE a legend is added on the right side
legend_breaks

Number of displayed breaks / labels in the legend. Needs an integer giving the desired number of breaks as input. Breakpoints are internally calculated by R's pretty() function, which can also lead to values slightly smaller or larger than the desired number.
legend_title

Defines the title of the legend.
legend_position

Defines position of the legend. Choose either 'bottom', right', 'left' or 'top'.
legend_point_sizes

Defines the size of the symbols representing the total NA bubbles in the legend.

You can choose between "default", "actual" or a custom vector of sizes.

  • "default" - Scales the points in the legend to symbolically resemble the size differences (default choice)

  • "actual" - Scales the points in the legend according to their actual size in the plot

Since these two options are not be always sufficient, a custom vector of sizes can be used as input. This would look like this: c(4,5,6,7). Be aware, that the length of this vector must match the number of breakpoints (can be adjusted with legend_breaks).
theme

Set a theme for ggplot2. Default is ggplot2::theme_linedraw(). (theme_linedraw)

Value

The output is a ggplot2 object that can be further adjusted by using the ggplot syntax

Details

This function can be used to visualize the total NA counts for individual NA gap sizes (NAs in a row) in a time series. The bubble plot makes it easy to see, which gap sizes account for most of the NAs in the series. The size and color of the bubbles represents the total NAs a certain gap size accounts for.

Total NAs for a gap size is calculated the following: total NAs = occurrence * gap length

You could e.g. interpret a bubble for gap size 2 the following: A 2 NA-gap (2 NAs in a row) occurred 27 times in the time series and thus was responsible for 54 total NAs.

On the x-axis the different gap sizes are plotted in increasing order. The y-axis shows the occurrence count of these gap sizes in the time series.

The plot is useful for finding out more about possible root causes of the missing data. It can give an indication, if the missing data appears randomly or if there are certain patterns of interest.

Dependent on the time series input, there might be too much information in the plot, which leads to overplotting issues. In these cases, using the min_totals, min_occurrence, min_gapsize parameters can be used to display only the information of interest.

The only really needed parameter for this function is x (the univariate time series with NAs that shall be visualized). All other parameters are solely for altering the appearance of the plot.

As long as the input is univariate and numeric, the function also takes data.frame, tibble, tsibble, zoo, xts as an input.

The plot can be adjusted to your needs via the function parameters. Additionally, for more complex adjustments, the output can also be adjusted via ggplot2 syntax. This is possible, since the output of the function is a ggplot2 object. Also take a look at the Examples to see how adjustments are made.

See also

ggplot_na_distribution, ggplot_na_distribution2, ggplot_na_gapsize, ggplot_na_level, ggplot_na_level2

Author

Steffen Moritz

Examples

# Example 1: Visualize total NA counts in tsNH4
ggplot_na_gapsize2(tsNH4)


# Example 2: Visualize total NA counts in tsNH4, different color gradient
ggplot_na_gapsize2(tsNH4, colors_bubbles = rev(grDevices::heat.colors(10)))


# Example 3: Same as example 1, just written with pipe operator
tsNH4 %>% ggplot_na_gapsize2()


# Example 4: Visualize total NA counts in tsHeating
# Limited to gap sizes that account for a total of > 600 NAs
ggplot_na_gapsize2(tsHeating, min_totals = 600)


# Example 5: Visualize total NA counts in tsNH4 - no legend
ggplot_na_gapsize2(tsNH4, legend = FALSE)


# Example 6: Visualize total NA counts in tsAirgap - increased bubble size
ggplot_na_gapsize2(tsAirgap, size_bubbles = 35)


# Example 7: Visualize total NA counts in tsNH4
# Plot adjustments via ggplot_na_gapsize2 function parameters
ggplot_na_gapsize2(tsNH4, theme = ggplot2::theme_classic())


# Example 8: Visualize total NA counts in tsNH4 - title, subtitle in center
# Plot adjustments via ggplot2 syntax
ggplot_na_gapsize2(tsNH4) +
  ggplot2::theme(plot.title = ggplot2::element_text(hjust = 0.5)) +
  ggplot2::theme(plot.subtitle = ggplot2::element_text(hjust = 0.5))


# Example 9: Visualize total NA counts in tsNH4 - title in center, no subtitle
# Plot adjustments via ggplot2 syntax and function parameters
ggplot_na_gapsize2(tsNH4, subtitle = NULL) +
  ggplot2::theme(plot.title = ggplot2::element_text(hjust = 0.5))


# Example 10: Total NA counts in tsNH4 - legend on the bottom and color change
# Plot adjustments via ggplot2 syntax and function parameters
ggplot_na_gapsize2(tsNH4, colors_bubbles = grDevices::heat.colors(10)) +
  ggplot2::theme(legend.position = "bottom")