sp_rda: Generate RDA plot with species table and env table

In Tong-Chen/ImageGP: For ImageGP cloud platform (https://www.bic.ac.cn/BIC)

Generate RDA plot with species table and env table

Description

Generate RDA plot with species table and env table

Usage

sp_rda(
  otu_table,
  env_table,
  metadata,
  sample_min_reads_count = 10000,
  rare_otu_count = 5,
  otu_scale_method = "hellinger"
)

Arguments

otu_table	Normalized OTU/Species abundance data frame or data file (with header line, the first column will be treated as the row names, tab separated)
env_table	Environment factor data frame or data file (with header line, the first column will be treated as the row names, tab separated)
metadata	Metadata file (or data.frame) with sample attributes like group information. The first column is the same as the first row of value given to parameter data. These attributes would be used as color, size, shape variables in the plot. If not supplied, each sample will be treated as one group.
sample_min_reads_count	The minimum allowed sample reads count. Default 10000 meaning samples with total reads count less than 10000 would be filtered.
rare_otu_count	Definite rare OTU. OTU with abundance in all samples less than given value would be filtered.
otu_scale_method	Popular (and effective) standardization methods for community ecologists like total, max, frequency, normalize, range, rank, rrank, standardize, hellinger, chi.square, rclr, log, clr, alr.
...	Parameters given to sp_ggplot_layout

Value

A ggplot2 object

Examples

## Not run:
input <- "KO-OE_all.txt"
volcano_plot(input,log2fc_var='Log2FoldChange',fdr_var='Padj',status_col_var='',
             title="sd",label="Label",log10_transform_fdr=TRUE,point_size=5)
## End(Not run)

Tong-Chen/ImageGP documentation built on April 14, 2025, 12:54 p.m.