Draw an interactive network plot for a network meta-analysis

Draws the network of treatment comparisons from arm level data. Each node is a treatment and each line joins two treatments compared directly in at least one study. Hovering over a node shows a compact table of every arm on that treatment; hovering over a line shows the arms of each study that makes that comparison. The card holds the columns named in hover. Clicking either opens a panel under the plot with the full arm level data side by side, one column per arm, in the manner of a trial's baseline table: every column of data other than study, treatment and group becomes a row, so baseline characteristics and outcomes are shown as they were given.

Usage

ggnma(
  data,
  study,
  treatment,
  n = NULL,
  group = NULL,
  hover = NULL,
  multiarm = TRUE,
  positions = NULL,
  palette = NULL,
  legend = TRUE,
  legend_title = NULL,
  title = NULL,
  caption = NULL,
  family = "Lato",
  contributions = NULL
)

Arguments

data: A data frame with one row per study arm.
study, treatment: Bare column names identifying the study and the treatment of each arm. Each treatment may appear once per study.
n: Optional bare column giving the number of participants in each arm. Sets node area and the participant counts in the hover cards.
group: Optional bare column naming a class for each treatment, such as a drug class. Nodes are then colored by class and a legend is drawn. Each treatment must belong to exactly one class.
hover: Names of the columns shown in the hover card, one row each, such as the sample size, an outcome and a key baseline characteristic. Defaults to the first four columns of the arm table. Use character(0) for a card that only lists the studies. The click panel always shows every column.
multiarm: Shade a polygon for each set of treatments compared in a study with more than two arms.
positions: Optional data frame placing the nodes by hand, with columns treatment, x and y, one row per treatment and y pointing up. Any units will do: the layout is scaled to fit the plot, keeping its shape. Labels point away from the middle of the layout.
palette: Node colors. With group, a vector named by class, or an unnamed vector recycled over the classes; without it, a single color. Defaults to race_palette().
legend: Draw the legend when group is given.
legend_title: Text in front of the legend, such as "Class".
title, caption: Title above the plot and note below it.
family: Font family. The package ships Lato and registers it on load.
contributions: Show where the evidence for each comparison comes from: a fit from netmeta::netmeta() on the same network, whose contributions are then computed with netmeta::netcontrib(), or an object that function returned. The widget gains a menu of every comparison; picking one widens and colors each line by the share of that network estimate flowing through it, labels the shares and says them in words under the plot.

Value

An object of class ggnma, which prints as an interactive widget. Use graph_widget(), graph_plot() or graph_save() for the widget, a static ggplot or a file. The fields nodes and edges hold the treatments and comparisons with their study counts, multiarm the sets of treatments compared in multi-arm studies, and width and height the natural size in inches. With contributions, the field contributions holds the shares.

Details

Treatments sit on a circle, starting at the top and running clockwise in the order of the levels of treatment when it is a factor, or in order of first appearance otherwise; positions places them by hand instead. Line width follows the number of studies that make the comparison. When n is given, node area follows the total number of participants on that treatment. A study with more than two arms adds a line for every pair of its treatments and, with multiarm, a shaded polygon joining them. Studies that compare the same set of treatments share one polygon, which has its own hover card and panel.

Row labels come from each column's label attribute when it has one, as set by the 'labelled', 'Hmisc' or 'haven' packages, and otherwise from its name. Text that contains a URL or a DOI, such as a reference column, is linked in the panel.

Examples

net <- ggnma(psoriasis_nma, study, treatment, n = n, group = class,
             legend_title = "Class")
net
net$edges
#>                 from                 to studies    n
#> 1            Placebo         Etanercept       1  652
#> 2            Placebo Secukinumab 150 mg       4 1386
#> 3            Placebo Secukinumab 300 mg       4 1385
#> 4         Etanercept Secukinumab 150 mg       1  653
#> 5         Etanercept Secukinumab 300 mg       1  653
#> 6        Ustekinumab Secukinumab 300 mg       1  676
#> 7 Secukinumab 150 mg Secukinumab 300 mg       4 1383

# \donttest{
if (requireNamespace("netmeta", quietly = TRUE) &&
    requireNamespace("meta", quietly = TRUE)) {
  pw <- meta::pairwise(treat = treatment, event = pasi75_r, n = pasi75_n,
                       studlab = study, data = psoriasis_nma, sm = "OR")
  fit <- netmeta::netmeta(pw, common = FALSE)
  ggnma(psoriasis_nma, study, treatment, n = n, contributions = fit)
}
# }