scatter_plot: Scatter plot for NCM results and data frames

In ncmR: Fit Neutral Community Model to Microbiome or Ecological Data

Scatter plot for NCM results and data frames

Description

Generic function for creating scatter plots. Methods available for NCM result objects and data frames.

Usage

scatter_plot(object, ...)

## S3 method for class 'NCM'
scatter_plot(
  object,
  point_alpha = 0.8,
  point_size = 3,
  point_colors = c(Above = "#ED7D70", Below = "#2B889B", Neutral = "#B57FAF"),
  fit_line_color = "#335399",
  fit_line_type = "solid",
  fit_line_size = 1,
  ci_line_color = "#335399",
  ci_line_type = "dashed",
  ci_line_size = 1,
  axis_title_x_text = "Mean relative abundance (log10)",
  axis_title_y_text = "Frequency of occupancy",
  axis_title_x_size = 25,
  axis_title_y_size = 25,
  axis_text_x_size = 20,
  axis_text_y_size = 20,
  legend_title_text = NA,
  legend_size = 6,
  legend_position = c(0.8, 0.4),
  legend_hjust = 0,
  legend_vjust = 1,
  fit_para_size = 6,
  fit_para_position = c(0.02, 0.98),
  fit_para_hjust = 0,
  fit_para_vjust = 1,
  font_family = "sans",
  ...
)

## S3 method for class 'data.frame'
scatter_plot(
  object,
  rsqr,
  Nm,
  m,
  map,
  point_alpha = 0.8,
  point_size = 3,
  point_colors = c(Above = "#ED7D70", Below = "#2B889B", Neutral = "#B57FAF"),
  fit_line_color = "#335399",
  fit_line_type = "solid",
  fit_line_size = 1,
  ci_line_color = "#335399",
  ci_line_type = "dashed",
  ci_line_size = 1,
  axis_title_x_text = "Mean relative abundance (log10)",
  axis_title_y_text = "Frequency of occupancy",
  axis_title_x_size = 25,
  axis_title_y_size = 25,
  axis_text_x_size = 20,
  axis_text_y_size = 20,
  legend_title_text = NA,
  legend_size = 6,
  legend_position = c(0.8, 0.4),
  legend_hjust = 0,
  legend_vjust = 1,
  fit_para_size = 6,
  fit_para_position = c(0.02, 0.98),
  fit_para_hjust = 0,
  fit_para_vjust = 1,
  font_family = "sans",
  ...
)

## Default S3 method:
scatter_plot(object, ...)

Arguments

object	An object to plot: NCM result or data.frame
...	Additional arguments passed to methods
point_alpha	Alpha transparency for points (default: 0.8)
point_size	Point size (default: 3)
point_colors	Named vector of colors for Above/Below/Neutral status
fit_line_color	Fitted line color (default: "#335399")
fit_line_type	Line type for fitted curve (default: "solid")
fit_line_size	Line width for fitted curve (default: 1)
ci_line_color	Confidence interval line color (default: "#335399")
ci_line_type	Confidence interval line type (default: "dashed")
ci_line_size	Confidence interval line width (default: 1)
axis_title_x_text	X-axis title text
axis_title_y_text	Y-axis title text
axis_title_x_size	X-axis title font size (default: 25)
axis_title_y_size	Y-axis title font size (default: 25)
axis_text_x_size	X-axis tick label font size (default: 20)
axis_text_y_size	Y-axis tick label font size (default: 20)
legend_title_text	Legend title text (default: NA)
legend_size	Legend text size (default: 6)
legend_position	Legend position as NPC coordinates c(x, y) (default: c(0.80, 0.40))
legend_hjust	Legend horizontal justification (default: 0)
legend_vjust	Legend vertical justification (default: 1)
fit_para_size	Fitting parameter text size (default: 6)
fit_para_position	Parameter annotation position as NPC coordinates c(x, y) (default: c(0.02, 0.98))
fit_para_hjust	Parameter horizontal justification (default: 0)
fit_para_vjust	Parameter vertical justification (default: 1)
font_family	Font family (default: "sans")
rsqr	R-squared value from NCM fit
Nm	Nm parameter from NCM fit
m	m parameter from NCM fit
map	Named vector for column name mapping (e.g., c(p = "abundance"))

Value

A ggplot object

Methods (by class)

• scatter_plot(NCM): Plot NCM result with fitted curve, confidence intervals, and parameter annotations. Supports full customization of visual elements.

• scatter_plot(data.frame): Plot data.frame by converting to NCM object. Requires manual specification of model parameters (rsqr, Nm, m) and optional column name mapping.

• scatter_plot(default): Default method for unsupported types.

Examples

# Load example data
data(example_data)
otu <- example_data$otu

# fit the total model using all samples
res_total <- fit_ncm(otu)

# plot
scatter_plot(res_total)

# Load example data
data(example_data)
otu <- example_data$otu

# fit the total model using all samples
res_total <- fit_ncm(otu)

df <- res_total$predictions

# Plot with manual parameters
scatter_plot(df, rsqr = 0.95, Nm = 500, m = 0.5678)

ncmR documentation built on April 19, 2026, 5:07 p.m.