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Controlling Plot Aesthetics

Source: vignettes/plot_aesthetics.Rmd
plot_aesthetics.Rmd

Controlling plot aesthetics is straightforward in dabestr. A key feature of dabestr is the ability for users to freely customize various components of a dabestr estimation plot, allowing for the creation of an optimal-looking plot.

Getting started

At this point, it is assumed that you have already obtained the effectsize object named dabest_effectsize_obj. To add and customize specific plot components, include them as arguments in the dabest_plot() function.

dabest_plot(
  dabest_effectsize_obj,
  float_contrast = TRUE,
  plot_component = "adjustment_value"
)

Adjusting Text

All text elements in the estimation plot can be modified. This includes the value, the size and even the removal of the text elements completely.

Size

The following parameters are responsible for adjusting the size of the text elements.

  • swarm_x_text: Numeric value determining the font size of the x-axis of the swarm plot. The default value is 11.
  • swarm_y_text: Numeric value determining the font size of the y-axis of the swarm plot. The default value is 15.
  • contrast_x_text: Numeric value determining the font size of the x-axis of the contrast plot. The default value is 11.
  • contrast_y_text:Numeric value determining the font size of the y-axis of the contrast plot. The default value is 15.

Check how the size has been changed in this example:

dabest_plot(
  dabest_twogroup_obj.mean_diff,
  float_contrast = TRUE,
  swarm_x_text = 30,
  swarm_y_text = 1,
  contrast_x_text = 30,
  contrast_y_text = 5
)

Content

The following parameters are responsible for adjusting the content of the text elements.

  • swarm_label: string value for the label of the y-axis in the swarm plot. This is the default “value” or “proportion of success” for proportion plots.
  • contrast_label: string value for the label of the y-axis in the contrast plot. This is the default “effect size” based on the effect sizes as given in effect_size().
  • delta2_label: string value for the label of the y-axis in the swarm plot. The default value is NULL.
dabest_plot(
  dabest_twogroup_obj.mean_diff,
  float_contrast = TRUE,
  swarm_label = "I love estimation statistics.",
  contrast_label = "I love it more than you do!"
)

Adjusting Visual Elements

Visual elements in dabestr refer to the shapes, lines, symbols or other visual representations that convey data and relationship in a plot. Many of these elements can be adjusted in dabestr.

Markers

The following parameters are responsible for adjusting the properties of various markers in the plot.

  • raw_marker_size: Numeric value determining the size of the points used in the swarm plot. The default value is 1.5.
  • raw_marker_alpha: Numeric value determining the transparency of the points in the swarm plot. The default value is 1.
  • raw_bar_width: Numeric value determining the width of the bar in the Sankey diagram. The default value is 0.3.
  • raw_marker_spread: The distance between the points if it is a swarm plot. The default value is 2.
  • raw_marker_side_shift: The horizontal distance that the swarm plot points are moved in the direction of the asymmetric_side. The default value is 0.
  • tufte_size: Numeric value determining the size of the tufte line in the swarm plot. The default value is 0.8.
  • es_marker_size: Numeric value determining the size of the points used in the delta plot. The default value is 0.5.
  • es_line_size: Numeric value determining the size of the ci line in the delta plot. The default value is 0.8.
A <- dabest_plot(dabest_twogroup_obj.mean_diff,
  float_contrast = TRUE,
  swarm_label = "", contrast_label = "",
  raw_marker_size = 1, raw_marker_alpha = 1
)
B <- dabest_plot(dabest_twogroup_obj.mean_diff,
  float_contrast = TRUE,
  swarm_label = "", contrast_label = "",
  raw_marker_size = 2, raw_marker_alpha = 0.5
)

cowplot::plot_grid(
  plotlist = list(A, B),
  nrow = 1,
  ncol = 2,
  labels = "AUTO"
)

Axes

The following parameters are responsible for adjusting the y-axis limits for both the raw data and contrast axes of the plot. By modifying the range, it creates the effect of zooming in or out of the plot.

  • swarm_ylim: Vector containing the y-limits for the swarm plot. The default value is NULL.
  • contrast_ylim: Vector containing the y-limits for the delta plot. The default value is NULL.
  • delta2_ylim: Vector containing the y-limits for the delta-delta plot. The default value is NULL.

If your effect size is qualitatively inverted (i.e., a smaller value indicates a better outcome), you can invert the vector passed to contrast_ylim.

dabest_plot(dabest_multigroup_obj.mean_diff,
  float_contrast = FALSE,
  contrast_label = "More negative is better!",
  swarm_ylim = c(1, 5), contrast_ylim = c(0.7, -1.2)
)

Palettes

The following parameters are responsible for adjusting the plot palettes of the plot.

  • custom_palette: string to set the colour palette. The default value is “d3”. The following palettes are also available: npg, aaas, nejm, lancet, jama, jco, ucscgb, d3, locuszoom, igv, cosmic, uchicago, brewer, ordinal and viridis_d.
npg <- dabest_plot(dabest_unpaired_props.mean_diff,
  swarm_label = "", contrast_label = "",
  custom_palette = "npg"
)
nejm <- dabest_plot(dabest_unpaired_props.mean_diff,
  swarm_label = "", contrast_label = "",
  custom_palette = "nejm"
)
jama <- dabest_plot(dabest_unpaired_props.mean_diff,
  swarm_label = "", contrast_label = "",
  custom_palette = "jama"
)
locuszoom <- dabest_plot(dabest_unpaired_props.mean_diff,
  swarm_label = "", contrast_label = "",
  custom_palette = "locuszoom"
)

cowplot::plot_grid(
  plotlist = list(npg, nejm, jama, locuszoom),
  nrow = 2,
  ncol = 2
)

Misc

  • sankey: this is a boolean value determining if the flows between the bar charts will be plotted. The default value is TRUE.
dabest_plot(dabest_paired_props.mean_diff, sankey = FALSE, raw_bar_width = 0.15)

  • flow: this is a boolean value determining whether the bars will be plotted in pairs. The default value is TRUE.
dabest_plot(dabest_paired_props.mean_diff, flow = FALSE, raw_bar_width = 0.15)

  • asymmetric_side: this is a string value that controls at which side the swarm points are shown. Accepted values are: “right” or “left”. The default one is “right”.
right <- dabest_plot(dabest_twogroup_obj.mean_diff,
  float_contrast = FALSE,
  swarm_label = "", contrast_label = "",
  asymmetric_side = "right"
)
left <- dabest_plot(dabest_twogroup_obj.mean_diff,
  float_contrast = FALSE,
  swarm_label = "", contrast_label = "",
  asymmetric_side = "left"
)

cowplot::plot_grid(
  plotlist = list(right, left),
  nrow = 1,
  ncol = 2
)

  • show_delta2: this is a boolean value determining if the delta-delta plot is shown. The default value is FALSE.
  • show_mini_meta: this is a boolean value determining if the weighted average plot is shown. When FALSE, the resulting graph would be identical to a multiple two-groups plot. The default value is FALSE.
  • show_zero_dot: this is a boolean value determining if there is a dot on the zero line of the effect size for the control-control group. The default value is TRUE.
  • show_baseline_ec: this is a boolean value determining whether the baseline curve is shown. The default value is FALSE.
dabest_plot(dabest_multigroup_obj.mean_diff,
  float_contrast = FALSE,
  show_baseline_ec = TRUE
)