mmeta (version 3.0.1)

MultipleTables.plot: Plot Method for Multipletables objects

Description

Produces a variety of plots for multiple tables analysis

Usage

MultipleTables.plot(
  multiple_tables_object,
  plot_type = "forest",
  layout_type = "overlay",
  selected_study_names = NULL,
  xlim = NULL,
  add_vertical = NULL,
  show_CI = TRUE,
  by = "line_type"
)

Value

A ggplot2 object is returned.

Arguments

multiple_tables_object

The object inheriting from class Multipletables.

plot_type

a character string specifying the kind of plots to produce. Options are density and forest (default). See details

layout_type

a character string specifying the type of the density plots (i.e., when plot_type=‘density’). Options are sidebyside and overlay (default). This argument is NULL when plot_type=‘forest’

selected_study_names

a numeric value or vector specifying which studies to be plotted. By default (when NULL), all of the studies will be plotted.

xlim

a numeric value specifying the lower and upper limits of the x-axis. Default is NULL. For forest plots, if the lower bound of any measure is smaller than xlim[1] or the upper bound of any measure is larger than xlim[2], arrows will be used at the limits to denote the bounds exceed the specified ranges.

add_vertical

a numeric value specifying the x-value for a vertical reference line at x=addline. Default is NULL.

show_CI

a logical value; If TRUE (default) the forest plot will show the lower & upper bounds of CIs, else the the lower & upper bounds of CIs will be omitted. This argument is always NULL when plot_type=‘density’.

by

a character string specifying the way to distinguish different plots. Options are line_type (default) and color.

Details

If plot_type=‘density’ and layout_type='sidebyside', the posterior distributions of all study-specific measure are displayed side by side in 4-panel plots with study names.

If plot_type=‘density’ and layout_type='overlap', the posterior distributions of all study-specific measure are displayed in one graph. To clarity, it is advisable to specify a few studies by selected_study_names argument.

If type='forest') and layout_type='NULL', a forest plot of all study-specific and overall measure with 95% credible/confidence intervals are plotted.

See Also

MultipleTables.create, MultipleTables.modelFit, and MultipleTables.summary.

Examples

# \donttest{
 library(mmeta)
 library(ggplot2)
 ## Analyze the dataset colorectal to conduct exact inference of the odds ratios
 data(colorectal)
 colorectal['study_name'] <- colorectal['studynames']
 ## If exact method is used, the codes for sampling method are similar.
 ## Create object multiple_tables_obj_exact
 multiple_tables_obj_exact <- MultipleTables.create(data=colorectal,
  measure='OR', model= 'Sarmanov')
 ## Model fit default
 multiple_tables_obj_exact <- MultipleTables.modelFit(multiple_tables_obj_exact, method = 'exact')
 ## Summary of the fitting process (default)
 multiple_tables_obj_exact <- MultipleTables.summary(multiple_tables_obj_exact)
 ## Density plot, overlay
 ## Note: There are no enough types of line, if we have too many densities!
 MultipleTables.plot(multiple_tables_obj_exact, plot_type = 'density',
 layout_type = 'overlay')
 ## Choose Set by = ‘color’
 MultipleTables.plot(multiple_tables_obj_exact, plot_type = 'density',
 layout_type = 'overlay',by = 'color')
 ## Set by = ‘color’ and specify xlim as 0 to 5.
 MultipleTables.plot(multiple_tables_obj_exact, plot_type = 'density',
 layout_type = 'overlay', by = 'color', xlim = c(0,5))
 ## Set by = ‘color’ and specify xlim as 0 to 5 and add vertical line at OR = 1
 MultipleTables.plot(multiple_tables_obj_exact, plot_type = 'density',
 layout_type = 'overlay', by = 'color',xlim = c(0,5), add_vertical = 1)
 ## If select three studies
 MultipleTables.plot(multiple_tables_obj_exact, plot_type = 'density',
 layout_type = 'overlay',selected_study_names = c('Bell','Chen','Oda'), xlim = c(0,5))
 ## We can add external layouts for the return ggplot2. xlab as Odds ratio
 ggplot2_obj <- MultipleTables.plot(multiple_tables_obj_exact,
 plot_type = 'density', layout_type = 'overlay', by = 'color',xlim = c(0,5))
 ggplot2_obj + xlab('Odds Ratio')  + ggtitle('OR ration for XX cancer')
 ## density plot, plot side by side
 MultipleTables.plot(multiple_tables_obj_exact, plot_type = 'density',
 layout_type = 'side_by_side')
 ## Forest plot (default)
 MultipleTables.plot(multiple_tables_obj_exact, plot_type = 'forest')
 ## forest plot: not show the CIs
 MultipleTables.plot(multiple_tables_obj_exact, plot_type = 'forest',
 add_vertical =  1, show_CI = FALSE)
# }