BinMat (version 0.1.1)

nmds: Creates a non-metric multidimensional scaling plot (nMDS).

Description

Creates an non-metric multidimensional scaling plot from a consolidated binary matrix with grouping information. Colours and shapes of plotted points need to be specified. For example, if there are two groups, then: clrs = c("red", "blue"), sh = c(16, 16). This assigns red to the first group name, and blue to the second. Both will have a pch shape of 16 (round dot). These two vectors are then passed to the function nmds() as: colours = clrs, shapes = sh.

Usage

nmds(
  x,
  dist_meth = "binary",
  k_val = 2,
  pt_size = 1,
  colours,
  shapes,
  labs = FALSE
)

Arguments

x

Consolidated binary matrix with grouping information in the second column.

dist_meth

Distance method. Set to "binary" by default. Other options are "euclidean", "maximum", "manhattan", "canberra", or "minkowski".

k_val

Number of dimensions for the nMDS plot. Set to 2 by default.

pt_size

Point size for symbols on the plot. Set to 1 by default.

colours

Vector containing colours to be assigned to groups.

shapes

Vector containing pch values for shapes to be used for points.

labs

Indicate whether labels should appear on the graph or not (TRUE or FALSE). Default = FALSE.

Value

nMDS plot.

Examples

# NOT RUN {
 mat = BinMatInput_ordination
group.names(mat)
clrs = c("red", "green", "black")
shp = c(16,16,16)
nmds(mat, colours = clrs, shapes = shp, labs = TRUE)

# }