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Forest plot individual and combined TWIST/GMTE estimates

Source: R/gmte_plot.R
gmte_plot.Rd

Plot the individual and combined estimates from a Triangulation WIthin A STudy (TWIST) analysis. The gmte_plot function takes an object of class twistR_GMTE, containing effect estimates from the individual tests (such as RGMTE) and the results when combinations are performed (such as RGMTE+MR), and creates a forest plot, highlighting the individual and combined estimates, and indicating with a "*" when the combined estimate may be valid.

Usage

gmte_plot(
  x,
  plot_title = "",
  plot_cat = TRUE,
  cols = c("#f46036", "#2e294e", "#1b998b"),
  pchs = c(15, 16, 23)
)

Arguments

x

An object of class twistR_GMTE e.g., the output from gmte_continuous

plot_title

A string to print as the plot title

plot_cat

Logical. Plot the CAT estimates? (Default=TRUE)

cols

Three colours to indiciate the three model types (GMTE0, individual estimates, combined estimates)

pchs

Three point types to indiciate the three model types (GMTE0, individual estimates, combined estimates)

References

Bowden, J., et al., The Triangulation WIthin A STudy (TWIST) framework for causal inference within Pharmacogenetic research. PLoS Genetics. https://doi.org/10.1371/journal.pgen.1009783

Author

Jack Bowden; Luke Pilling.

Examples

# Example using a continuous outcome (LDL), binary treatment (statins), and binary genotype (SLCO1B1*5 homozygotes) variables
Y="ldl"
T="statin"
G="slco1b1_5_hmz"
Z="age+PC1+PC2+PC3+PC4+PC5+PC6+PC7+PC8+PC9+PC10"
results=gmte_continuous(Y,T,G,Z,D)
#> TWIST (Triangulation WIthin A STudy) analysis in R - continuous outcome
#> Error in gmte_continuous(Y, T, G, Z, D): D needs to be a data.frame

gmte_plot(results, plot_title = "SLCO1B1*5 effect on LDL during statin treatment")
#> Error in eval(expr, envir, enclos): object 'results' not found

# If desired, remove CAT estimates for "cleaner" plot, as these are often orders of magnititude larger than the other estimates
gmte_plot(results, plot_title = "SLCO1B1*5 effect on LDL during statin treatment", plot_cat=FALSE)
#> Error in eval(expr, envir, enclos): object 'results' not found