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]