Scater Plot

Scater Plot

Arguments

x

phyloseq-class object.

x_numeric

A column in sample_data to compare that is a numeric

y_numeric

A column in sample_data to compare that is a numeric

color_var

A column in sample_data to color points

point_size

geom_point. Default is 3

point_opacity

ggplot2 alpha value. Default is 0.5

point_shape

ggplot2 point shape value. Default is 21

side_panel

Logical. If side density to plot. Default is TRUE

side_panel_scale

ggside ggside.panel.scale requires a scalar numeric. default is 0.3

Value

a ggplot object.

Details

A simple plotting utility for visualization of two numerical variables. Provided two numerical variable present in sample_data of a phyloseq-class object, a scatter plot is returned.

References

Shetty SA (2021). Data visualization for microbiome analytics. https://github.com/microsud/biomeViz

Author

Sudarshan A. Shetty

Examples

library(biomeUtils)
library(biomeViz)
library(dplyr)
library(microbiome)
library(ggplot2)
ps <- FuentesIliGutData
plotScatterViz(ps, x_numeric = "age", y_numeric = "BMI",
               color_var = "ILI") +
               scale_fill_manual(values=c("steelblue", "brown3", "grey70"))+
               scale_fill_manual(values=c("steelblue", "brown3", "grey70"))
#> Scale for 'fill' is already present. Adding another scale for 'fill', which
#> will replace the existing scale.
#> Warning: Removed 1 rows containing non-finite values (stat_density).
#> Warning: Removed 1 rows containing missing values (geom_point).