Add paths connecting points on a ggplot scatterplot

Useful for tracing a few select individuals over time on an ordination plot. Samples in phyloseq must be arranged in order of timepoint for the path connections to be drawn in the correct order! You can arrange the samples in timepoint order with ps_arrange.

add_paths(
  ggplot,
  id_var,
  id_values,
  mapping = NULL,
  arrow = grid::arrow(length = grid::unit(2, units = "mm")),
  ...
)

Arguments

ggplot: ggplot scatterplot such as the output of ord_plot
id_var: name of variable used to identify grouping of points
id_values: values of id_var variable used to identify groups of points to draw
mapping: ggplot aesthetics created by aes(), e.g. aes(colour = ?) - group is already set to id_var internally!
arrow: arrowhead to add to path, NULL for none
...: additional arguments passed to geom_path

Value

ggplot with added layer with geom_path

Examples

library(ggplot2)
data("dietswap", package = "microbiome")

# arrange by timepoint first (or whatever your own time variable is)
dietswap %>%
  ps_arrange(timepoint) %>%
  tax_fix() %>%
  tax_transform("clr", rank = "Genus") %>%
  ord_calc(method = "PCA") %>%
  ord_plot(colour = "timepoint", alpha = 0.5, size = 2) %>%
  add_paths(
    id_var = "subject", id_values = c("azl", "byn"),
    mapping = aes(colour = timepoint), linewidth = 1.5
    # size = 1.5 # size instead of linewidth in older ggplot2 versions
  )


# paths do NOT connect points in the correct order without arranging first
dietswap %>%
  tax_fix() %>%
  tax_transform("clr", rank = "Genus") %>%
  ord_calc(method = "PCA") %>%
  ord_plot(colour = "timepoint", alpha = 0.5) %>%
  add_paths(
    id_var = "subject", id_values = c("azl", "byn"),
    mapping = aes(colour = timepoint), linewidth = 1.5
    # size = 1.5 # size instead of linewidth in older ggplot2 versions
  ) +
  ggtitle("WRONG PATH ORDER", "use ps_arrange first!")