Customising the plot

The hardware and bandwidth for this mirror is donated by METANET, the Webhosting and Full Service-Cloud Provider.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]metanet.ch.

The returned object is a ggplot

Every call to mirror_slope_plot() returns a standard ggplot object. This means you customise it with the same + syntax you already use, rather than learning package-specific options.

p <- mirror_slope_plot(
  md,
  trt_colors      = mirror_palette("colorblind"),
  show_difference = TRUE,
  show_slowing    = TRUE
)

p +
  labs(subtitle = "Exploratory analysis") +
  theme(
    plot.background = element_rect(fill = "grey98", color = NA),
    axis.text       = element_text(size = 11)
  )
#> Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)): font family
#> not found in Windows font database
#> Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)): font family
#> not found in Windows font database
#> Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
#> family not found in Windows font database
#> Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
#> family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database

Palettes

mirror_palette() returns a two-colour vector for the reference and comparator arms. Three palettes are provided. The colourblind-safe palette is recommended for publication.

mirror_palette("default")
#> [1] "#6B6B6B" "#005CB9"
mirror_palette("colorblind")
#> [1] "#999999" "#0072B2"

# Reverse if you want the stronger colour on the reference arm
mirror_palette("colorblind", reversed = TRUE)
#> [1] "#0072B2" "#999999"

You may also pass any named or unnamed length-two vector of your own colours:

mirror_slope_plot(
  md,
  trt_colors      = c("#4D4D4D", "#1B7837"),
  show_difference = TRUE,
  show_slowing    = TRUE,
  title           = "Custom colours"
)
#> Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
#> family not found in Windows font database
#> Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
#> family not found in Windows font database
#> Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
#> family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database

Font scaling

base_size scales all text proportionally. Increase it for slides or posters, decrease it for dense multi-panel figures.

mirror_slope_plot(
  md,
  trt_colors      = mirror_palette("colorblind"),
  show_difference = TRUE,
  show_slowing    = TRUE,
  base_size       = 14,
  title           = "Larger base size for presentation"
)
#> Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)): font family
#> not found in Windows font database
#> Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)): font family
#> not found in Windows font database
#> Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)): font family
#> not found in Windows font database
#> Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
#> family not found in Windows font database
#> Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
#> family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database

Custom terminology

Supply outcome_label and benefit_label to match your therapeutic area. Note that supplying benefit_label uses that text verbatim; omit it to get the auto-computed \dQuote{X% less decline} form.

mirror_slope_plot(
  md,
  trt_colors      = mirror_palette("colorblind"),
  show_slowing    = TRUE,
  outcome_label   = "worsening",
  title           = "Custom outcome terminology"
)
#> Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
#> family not found in Windows font database
#> Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
#> family not found in Windows font database
#> Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
#> family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database

Combining multiple panels

The package renders one two-arm comparison per plot. To show several endpoints together, build each plot separately and combine them with a layout package such as patchwork. This keeps mirrorslope focused while giving you full control over the arrangement.

library(patchwork)

# A second endpoint
set.seed(9)
df2 <- df
df2$AVAL <- c(rbind(rep(0, n),
                    c(rnorm(n / 2, -8, 4), rnorm(n / 2, -5, 4))))
md2 <- prep_mirror_data(df2, trt_levels = c("Placebo", "Active"),
                        time_baseline = "Baseline", time_endpoint = "Week 24",
                        value_label = "% Change (Secondary Endpoint)")
md2 <- add_summary(md2, c("Placebo" = -8.1, "Active" = -4.8),
                   stat_label = "LS-Mean")
md2 <- add_difference(md2, estimate = 3.3, p_value = 0.04)

pa <- mirror_slope_plot(md,  trt_colors = mirror_palette("colorblind"),
                        show_difference = TRUE, show_slowing = TRUE,
                        title = "Primary endpoint")
pb <- mirror_slope_plot(md2, trt_colors = mirror_palette("colorblind"),
                        show_difference = TRUE, show_slowing = TRUE,
                        title = "Secondary endpoint")

pa / pb
#> Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
#> family not found in Windows font database
#> Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
#> family not found in Windows font database
#> Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
#> family not found in Windows font database
#> Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
#> family not found in Windows font database
#> Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
#> family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database
#> Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
#> font family not found in Windows font database

For a shared y-axis across panels, set the same y_lim on each plot so the scales align.

Saving for publication

Pass save_path to write the figure directly, or use ggplot2::ggsave() on the returned object. A vector format (PDF or SVG) is preferable for print; raster formats should be at least 300 dpi.

mirror_slope_plot(
  md,
  trt_colors      = mirror_palette("colorblind"),
  show_difference = TRUE,
  show_slowing    = TRUE,
  save_path       = "figure1.pdf",
  width           = 9,
  height          = 6
)

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.