MatCorPlot: Microbial matel text and env correcton with the plot to...
In taowenmicro/ggClusterNet:

MatCorPlot

R Documentation

Microbial matel text and env correcton with the plot to showing,from science peper.

Description

Microbial matel text and env correcton with the plot to showing,from science peper.

Usage

MatCorPlot(
  env.dat,
  tabOTU,
  distance = "bray",
  method = "metal",
  method.cor = "spearman",
  cor.p = 0.05,
  x = TRUE,
  y = TRUE,
  diag = T,
  sig = TRUE,
  siglabel = FALSE,
  shownum = TRUE,
  numpoint = 22,
  numpoint2 = 21,
  numsymbol = NULL,
  curvature = 0.2,
  lacx = "left",
  lacy = "bottom",
  range = 0.5,
  p.thur = 0.3,
  onlysig = TRUE
)

Arguments

`env.dat`	env table
`tabOTU`	OTU table conbined with list
`distance`	The defult, distance = "bray", method of microbiota distance
`method`	method for matel test
`x`	x axis label
`y`	y axis label
`diag`	diag label
`sig`	if show only sig value
`siglabel`	R2 value
`numpoint`	point type 22
`numpoint2`	point type 21
`numsymbol`	point adding e.g. 27
`lacx`	location of x axis
`lacy`	location of y axis
`range`	curve size
`p.thur`	sig value
`onlysig`	T or F
`p.threshold`	The defult, p.threshold=0.05, it represents significance threshold below 0.05.
`fill`	fill coulor of node

Value

ggplot object

Author(s)

Contact: Tao Wen 2018203048@njau.edu.cn Jun Yuan junyuan@njau.edu.cn Penghao Xie 2019103106@njau.edu.cn

References

Yuan J, Zhao J, Wen T, Zhao M, Li R, Goossens P, Huang Q, Bai Y, Vivanco JM, Kowalchuk GA, Berendsen RL, Shen Q Root exudates drive the soil-borne legacy of aboveground pathogen infection Microbiome 2018,DOI: doi: 10.1186/s40168-018-0537-x

Examples

data(ps)
library(phyloseq)
library(tidyverse)
ps1 = filter_taxa(ps, function(x) sum(x ) > 200 , TRUE);ps1
otu = as.data.frame(t(vegan_otu(ps1)))
mapping = as.data.frame( sample_data(ps1))
tabOTU1 = list(otu1 = otu,otu2 = otu,otu3 = otu)
data(env1)
MatCorPlot(
  env.dat = env1,
 tabOTU = tabOTU1,
  distance = "bray",
  method = "metal",
  x = F,
  y = F,
  diag = T,
  sig = TRUE,
  siglabel = FALSE,
  shownum = TRUE,
  numpoint = NULL,
  numsymbol = 27,
  lacx = "left",
  lacy = "bottom",
  range = 0.5,
  p.thur = 0.3,
  onlysig = F
)

taowenmicro/ggClusterNet documentation built on March 29, 2024, 1:32 a.m.