ggplot_spaghetti {microbiomeDASim}R Documentation

Spaghetti Plots using ggplot2

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")


[Package microbiomeDASim version 1.8.0 Index]