nmds {BinMat}

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

Description

Creates an nMDS 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 = c("dodgerblue", "black", "red", "green3", "orange", "darkblue", "gold2",
    "darkgreen", "darkred", "grey", "darkgrey", "magenta", "darkorchid", "purple",
    "brown", "coral3", "turquoise", "deeppink", "lawngreen", "deepskyblue", "tomato",
    "yellow", "yellowgreen", "royalblue", "olivedrab", "midnightblue", "indianred1",
    "darkturquoise"),
  labs = FALSE,
  legend_pos = "right",
  include_ellipse = FALSE,
  ellipse_type = "norm",
  dimension1 = 1,
  dimension2 = 2
)

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. This can be changed to the options available in the RColorBrewer palette set (e.g. "Set1"). See <http://applied-r.com/rcolorbrewer-palettes/> for more palette options. Alternatively, the colours can be set manually using, for example, c("red", "green", "blue"), thereby setting a colour for each group in your dataset. There are 28 default colours that will be set automatically to your groups.

labs

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

legend_pos

Indicate the position of the legend. Default = "right", but other options are "left", "bottom", "top", or "none"

include_ellipse

Indicate whether ellipses should be included around groups. Default = FALSE.

ellipse_type

Select the type of ellipses to include around groups. Options are "convex", "confidence", "t", "norm", and "euclid". See the ggpubr::ggscatter() function documentation for more details.

dimension1

Indicate the first dimension to plot (1, 2, or 3) for the x axis. If k = 2, the first two dimensions will automatically be plotted. If k = 3, select between the three.

dimension2

Indicate the second dimension to plot (1, 2, or 3) for the y axis

Value

nMDS plot.

Examples

 mat = BinMatInput_ordination
group.names(mat)
clrs = c("red", "green", "black")
nmds(mat, colours = clrs, labs = TRUE, include_ellipse = TRUE)