---
title: "2. Creating plots"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{2. Creating plots}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

# Plot

The most common use case for `EpiViz` is plotting effect estimates (e.g., betas or odds ratios) across multiple sectors.

Using the built-in datasets, we can create a three-track scatter plot with confidence intervals to compare different cohorts or exposures.

The following are required:

- **`estimate_column`**: The central value to plot.
- **`pvalue_column`**: Used to color significant results differently (filled vs. empty points).
- **`pvalue_adjustment`**: The threshold for significance (default is 0.05).
- **`lower_ci` & `upper_ci`**: Used to draw confidence interval segments.
- **`equal_axis`**: Set to `TRUE` if you want all tracks to share the same Y-axis limits.

```r
circos_plot(
  track_number = 3,
  track1_data = EpiViz_data1,
  track2_data = EpiViz_data2,
  track3_data = EpiViz_data3,
  track1_type = "points",
  track2_type = "points",
  track3_type = "points",
  label_column = "label",
  section_column = "class",
  estimate_column = "beta",
  pvalue_column = "pvalue",
  lower_ci = "lower_confidence_interval",
  upper_ci = "upper_confidence_interval",
  circle_size = 25
)
```

![](figures/3_track_points.svg){width=100%}

# Shared Axis Limits

When comparing multiple tracks, it can be useful to force all tracks to share the same Y-axis scale. This makes visual comparison easier by ensuring the same vertical distance represents the same magnitude across all tracks.

```r
circos_plot(
  track_number = 3,
  track1_data = EpiViz_data1,
  track2_data = EpiViz_data2,
  track3_data = EpiViz_data3,
  track1_type = "points",
  track2_type = "points",
  track3_type = "points",
  label_column = "label",
  section_column = "class",
  estimate_column = "beta",
  pvalue_column = "pvalue",
  lower_ci = "lower_confidence_interval",
  upper_ci = "upper_confidence_interval",
  equal_axis = TRUE,
  circle_size = 25
)
```

![](figures/3_track_points_equal.svg){width=100%}