plot_ord: Visualization of Ordination results with scatterplot

In HuaZou/MicrobiomeAnalysis: Data analysis toolkits in metagenomics

Visualization of Ordination results with scatterplot

Description

Show the result of Ordination using scatterplot.

Usage

plot_ord(
    reslist,
    variable,
    variable_name = NULL,
    variable_color = NULL,
    var_shape = NULL,
    var_shape_name = NULL,
    var_shape_value = NULL,
    display_test = FALSE,
    sample_label = FALSE,
    ellipse_type = c("none", "ellipse", "ellipse_CI" ,
                     "ellipse_groups", "ellipse_line"),
    sideboxplot = FALSE,
    point_size = 3,
    line_size = 0.3,
    ellipse_line_size = 0.5,
    geom_text_size = 5,
    theme_text_size = 8,
    theme_strip_size = 6,
    legend_position = c(0, 0),
    legend_justification = c(-0.02, -0.02),
    legend_title_size = 7,
    legend_text_size = 6,
    test_annotate_size = 4,
    geom_label_repel_size = 2,
    ...)

Arguments

reslist	(Required). list. Results of Ordination.
variable	(Optional). character. the variable for x-axis.
variable_name	(Optional). character. variable' names (default: NULL).
variable_color	(Optional). character. the color for plotting (default: NULL).
var_shape	(Optional). character. the variable for shape' column (default: NULL).
var_shape_name	(Optional). character. the shape' names (default: NULL).
var_shape_value	(Optional). character. the shape values (default: NULL).
display_test	(Optional). logical. whether to show pvalue of PERMANOVA & beta dispersion (default: FALSE).
sample_label	(Optional). logical. whether to show sample names (default: FALSE).
ellipse_type	(Optional). character. how to show scatter plot, including "none", "ellipse", "ellipse_CI" , "ellipse_groups" and "ellipse_line" (default: "none").
sideboxplot	(Optional). logical. whether to show side boxplot of axis (default: FALSE).
point_size	(Optional). numeric. point size of the scatterplot (default: 3).
line_size	(Optional). numeric. line size (default: 0.3).
ellipse_line_size	(Optional). numeric. ellipse line size (default: 0.5).
geom_text_size	(Optional). numeric. geom: text size (default: 5).
theme_text_size	(Optional). numeric. main theme: text size (default: 8).
theme_strip_size	(Optional). numeric. main theme: strip size (default: 6).
legend_position	(Optional). numeric. main legend: position (default: c(0, 0)).
legend_justification	(Optional). numeric. main legend: justification (default: c(-0.02, -0.02)).
legend_title_size	(Optional). numeric. main legend: title size (default: 7).
legend_text_size	(Optional). numeric. main legend: text size (default: 6).
test_annotate_size	(Optional). numeric. PERMANOVA text size (default: 4).
geom_label_repel_size	(Optional). numeric. main geom: label repel size (default: 2).
...	additional parameters.

Value

A scatterplot with boxplot to show the results of ordination

Author(s)

Created by Hua Zou (8/9/2022 Shenzhen China)

Examples

# phyloseq object
data("Zeybel_2022_gut")
ps_zeybel <- summarize_taxa(Zeybel_2022_gut, level = "Genus")
ord_result <- run_ord(
  object = ps_zeybel,
  variable = "LiverFatClass",
  method = "PCoA")

 pl <- plot_ord(
  reslist = ord_result,
  variable = "LiverFatClass",
  ellipse_type = "ellipse",
  sideboxplot = TRUE,
  sample_label = TRUE
  )
 pl

# SummarizedExperiment object
data("Zeybel_2022_protein")
Zeybel_2022_protein_imp <- impute_abundance(
  Zeybel_2022_protein,
  group = "LiverFatClass",
  ZerosAsNA = TRUE,
  RemoveNA = TRUE,
  cutoff = 20,
  method = "knn")
ord_result <- run_ord(
  object = Zeybel_2022_protein_imp,
  variable = "LiverFatClass",
  method = "PCA")

 pl <- plot_ord(
  reslist = ord_result,
  variable = "LiverFatClass",
  ellipse_type = "ellipse",
  sideboxplot = TRUE,
  sample_label = TRUE
  )
 pl

HuaZou/MicrobiomeAnalysis documentation built on May 13, 2024, 11:10 a.m.