ggpcoa: '"PCoA"' ordination plot
In wdy91617/ggords: Ordination Visualization

Description Usage Arguments Details Value Author(s) Examples

Output pcoa ordination plot.

ggpcoa(ord, ordata, groups = NULL, axes = c(1, 2), obslab = FALSE,
  moblabs = NULL, obssize = 2, obscol = "black", obspch = 16,
  obsFonts = "serif", obsface = "plain", spe = TRUE, msplabs = NULL,
  spearrow = 0.2, spelab = TRUE, spmapsize = NULL, spaline = 1,
  spalwd = 0.5, spacol = "grey30", sprotate = NULL, spesize = 4,
  specol = "red", spepch = 16, speFonts = "serif", speface = "plain",
  envs = NULL, mflabs = NULL, farrow = 0.2, fmapsize = NULL,
  faline = 1, falwd = 0.5, facol = "blue", fzoom = 1, frotate = NULL,
  fsize = 5, fcol = "blue", fFonts = "serif", fface = "plain",
  ellipse = FALSE, ellprob = 0.95, cirlwd = 1, cirline = 2)

`ord`	An object produced by `cmdscale`.
`ordata`	An dataframe that is provided to function `wascores`.
`groups`	An grouping factor, its length is the same as the row number of the ordination dataframe.
`axes`	Axes shown.
`obslab`	A logical value, obslab = FALSE(The row variables are displayed as points), obslab = TRUE(The row variables are displayed as texts).
`moblabs`	A vector of strings, rename the row variable names displayed.
`obssize`	The size of row variables.
`obscol`	The colour of row variables.
`obspch`	The point shape of row variables.
`obsFonts`	The family of row variables.
`obsface`	The fontface of row variables.
`spe`	A logical value, whether the column variables are displayed.
`msplabs`	A vector of strings, rename the col variable names displayed.
`spearrow`	Arrowhead length of col variables.
`spelab`	A logical value, spelab = FALSE(The col variables are displayed as points), spelab = TRUE(The col variables are displayed as texts).
`spmapsize`	Numeric value, the size of col variable labels is mapped by the length of arrowhead.
`spaline`	Type of arrowhead segment.
`spalwd`	Numeric value, the width of arrowhead segment.
`spacol`	The colour of arrowhead segment.
`sprotate`	Numeric value, rotation angle of col variable labels.
`spesize`	Numeric value, the size of col variable labels or points.
`specol`	The colour of col variable labels or opoints.
`spepch`	Type of col variable labels or points .
`speFonts`	The family of col variable labels.
`speface`	The fontface of col variable labels.
`envs`	Dataframe fitted.
`mflabs`	A vector of strings, rename the fitted variable names displayed.
`farrow`	Arrowhead length of fitted variables.
`fmapsize`	Numeric value, the size of fitted variable labels is mapped by the length of arrowhead.
`faline`	Arrowhead type of fitted variables.
`falwd`	Numeric value, arrowhead width of fitted variables.
`facol`	Arrowhead colour of fitted variables.
`fzoom`	Numeric value, scaling arrow length.
`frotate`	Numeric value, rotation angle of fitted variable labels.
`fsize`	Numeric value, the size of fitted variable labels or points.
`fcol`	The colour of fitted variable labels or opoints.
`fFonts`	The family of fitted variable labels.
`fface`	The fontface of fitted variable labels.
`ellipse`	A logical value, whether confidence ellipses are displayed.
`ellprob`	Numeric value, confidence interval.
`cirlwd`	Numeric value, line width of ellipse.
`cirline`	Line type of ellipse.

Control of some parts is put in the function. Theme of figure can be set by theme of ggplot2.

Returns a ggplot object.

Dongya Wang <wdy91617@163.com>

data(Envs)
library(vegan)
# get group factor
Env.w <- hclust(dist(scale(Envs)), "ward.D")
gr <- cutree(Env.w , k=4)
grl <- factor(gr)

# Compute PCoA
Env.bray <- vegdist(Envs)
Env.pcoa <- cmdscale(Env.bray, eig=TRUE)
summary(Env.pcoa)

# Produce a plot 
ggpcoa(Env.pcoa, ordata = Envs)

# Add a group
ggpcoa(Env.pcoa, ordata = Envs, group = grl) 

# Set a theme 
require(ggplot2)
ggpcoa(Env.pcoa, ordata = Envs, group = grl, fcol = "white", facol = "white") + theme_dark()

# Remove the arrow
ggpcoa(Env.pcoa, ordata = Envs, group = grl, spearrow = NULL)

# Modify legend title, group color and point shape
ggpcoa(Env.pcoa, group = grl, ordata = Envs, spearrow = NULL) + 
  scale_color_manual(name = "Groups",values = c("red2", "purple1", "grey20","cyan")) +
  scale_shape_manual(name = "Groups",values = c(8,15,16,17))

#Add confidence ellipses
ggpcoa(Env.pcoa, ordata = Envs, group = grl, spearrow = NULL, ellipse = TRUE) +
  scale_colour_hue(l = 70, c = 300)