ggflower: Use microbiome data to map petals

In taowenmicro/ggClusterNet:

Use microbiome data to map petals

Description

Use microbiome data to map petals

Usage

ggflower(
  otu = NULL,
  tax = NULL,
  map = NULL,
  ps = NULL,
  group = "Group",
  rep = 6,
  m1 = 2,
  start = 1,
  a = 0.2,
  b = 1,
  lab.leaf = 1,
  col.cir = "yellow",
  a.cir = 0.5,
  b.cir = 0.5,
  m1.cir = 2
)

Arguments

otu	otu table of microbiome. data.frame
tax	taxonmy table of microbiome. data.frame
map	table.data.frame
ps	phyloseq Object, contains OTU tables, tax table and map table, represented sequences,phylogenetic tree.
group	colnames which selected for show
rep	repeat number of microbial data.
m1	Petal shape, square to round to prismatic, the value gradually decreases
start	The rotation angle of the petals, the greater the value, the greater the angle
a	The width of the petals
b	Distance from petal to center
lab.leaf	The distance from the label to the center of the circle
col.cir	Center color

Value

ggplot objects

Author(s)

Contact: Tao Wen [e-mail] Jun Yuan [e-mail] Penghao Xie [e-mail]

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

library(phyloseq)
library(ggplot2)
data(ps)

map = as.data.frame(sample_data(ps))
map$Group1 <- c("A","B","C","D","E","F ")
sample_data(ps) = map

p <- ggflower(ps = ps,
              rep = 3,
              group = "Group1",
              start = 1,
              m1 = 2,
              a = 0.3,
              b = 0.3,
              lab.leaf = 1,
              col.cir = "yellow",
              b.cir = 0.8,
              a.cir = 0.8
)
p2 <- p + scale_fill_brewer(palette = "Paired")
p2
p <- ggflower(ps = ps,
              rep = 3,
              group = "Group1",
              start = 1,
              m1 = 1,
              a = 0.3,
              b = 1,
              lab.leaf = 1,
              col.cir = "yellow"
)
p3 <- p + scale_fill_brewer(palette = "Paired")

p3
p5 <- ggflower(ps = ps,
               rep = 3,
               group = "Group1",
               start = 1,
               m1 = 2,
               a = 0.2,
               b = 1,
               lab.leaf = 1,
               col.cir = "yellow"
)
p5

p <- ggflower(ps = ps,
              rep = 3,
              group = "Group1",
              start = 30,
              m1 = 2,
              a = 0.2,
              b = 1,
              lab.leaf = 1,
              col.cir = "yellow"
)
p1 <- p + scale_fill_brewer(palette = "Paired")

p1

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