ggplot_spaghetti: Spaghetti Plots using 'ggplot2'

In microbiomeDASim: Microbiome Differential Abundance Simulation

Description

This function allows the user to create spaghetti plots for individuals with time varying covariates. You can also break this down into subgroups to analyze different trentds.

Usage

ggplot_spaghetti(
  y,
  id,
  time,
  alpha = 0.2,
  method = "loess",
  jit = 0,
  group = NULL
)

Arguments

y	This is the y-axis parameter to specify. Generally it is a continuous variable.
id	This is the id parameter that identifies the unique individuals or units.
time	This is the time vector and must be numeric.
alpha	Scalar value between [0,1] that specifies the transparencey of the lineplots.
method	Character value that specifies which type of method to use for fitting. Optional methods come from geom_smooth function.
jit	Scalar value that specifies how much you want to jitter each individual observation. Useful if many of the values share the same y values at a time point.
group	Specifies a grouping variable to be used, and will plot it by color on one single plot.

Details

Note that the data must be in long format.

Value

Plots a time series data by each individual/unit with group trends overlayed.

Examples

library(ggplot2)
num_subjects_per_group <- 15
sim_obj <- mvrnorm_sim(n_control=num_subjects_per_group,
                       n_treat=num_subjects_per_group,
                       control_mean=5, sigma=1, num_timepoints=5,
                       t_interval = c(0, 4),
                       rho=0.95, corr_str='ar1', func_form='linear',
                       beta=c(0, 0.25),
                       missing_pct=0.6, missing_per_subject=2)

with(sim_obj$df, suppressWarnings(ggplot_spaghetti(y=Y_obs, id=ID, time=time,
                                                  jit=0.1, group=group)))+
  labs(title="Simulated Microbiome Data from Multivariate Normal",
       y="Normalized Reads", x="Time") +
  scale_linetype_manual(values=c("solid","dashed"), name="Group") +
  scale_color_manual(values=c("#F8766D", "#00BFC4"), name="Group")

microbiomeDASim documentation built on Nov. 8, 2020, 10:58 p.m.