nms_ord {supportR}

Publication-Quality Non-metric Multi-dimensional Scaling (NMS) Ordinations

Description

Produces Non-Metric Multi-dimensional Scaling (NMS) ordinations for up to 10 groups. Assigns a unique color for each group and draws an ellipse around the standard deviation of the points. Automatically adds stress (see vegan::metaMDS for explanation of "stress") as legend title. Because there are only five hollow shapes (see ?graphics::pch()) all shapes are re-used a maximum of 2 times when more than 5 groups are supplied.

Usage

nms_ord(
  mod = NULL,
  groupcol = NULL,
  title = NA,
  colors = c("#41b6c4", "#c51b7d", "#7fbc41", "#d73027", "#4575b4", "#e08214", "#8073ac",
    "#f1b6da", "#b8e186", "#8c96c6"),
  shapes = rep(x = 21:25, times = 2),
  lines = rep(x = 1, times = 10),
  pt_size = 1.5,
  pt_alpha = 1,
  leg_pos = "bottomleft",
  leg_cont = unique(groupcol)
)

Arguments

mod

Object returned by vegan::metaMDS

groupcol

(dataframe) column specification in the data that includes the groups (accepts either bracket or $ notation)

title

(character) string to use as title for plot

colors

(character) vector of colors (as hexadecimal codes) of length >= group levels (default not colorblind safe because of need for 10 built-in unique colors)

shapes

(numeric) vector of shapes (as values accepted by pch) of length >= group levels

lines

(numeric) vector of line types (as integers) of length >= group levels

pt_size

(numeric) value for point size (controlled by character expansion i.e., cex)

pt_alpha

(numeric) value for transparency of points (ranges from 0 to 1)

leg_pos

(character or numeric) legend position, either numeric vector of x/y coordinates or shorthand accepted by graphics::legend

leg_cont

(character) vector of desired legend entries. Defaults to unique entries in groupcol argument (this argument provided in case syntax of legend contents should differ from data contents)

Value

(base R plot) base R plot with ellipses for each group

Examples

# Use data from the vegan package
utils::data("varespec", package = 'vegan')
resp <- varespec

# Make some columns of known number of groups
factor_4lvl <- c(rep.int("Trt1", (nrow(resp)/4)),
                 rep.int("Trt2", (nrow(resp)/4)),
                 rep.int("Trt3", (nrow(resp)/4)),
                 rep.int("Trt4", (nrow(resp)/4)))

# And combine them into a single data object
data <- cbind(factor_4lvl, resp)

# Actually perform multidimensional scaling
mds <- vegan::metaMDS(data[-1], autotransform = FALSE, expand = FALSE, k = 2, try = 50)

# With the scaled object and original dataframe we can use this function
nms_ord(mod = mds, groupcol = data$factor_4lvl,
                title = '4-Level NMS', leg_pos = 'topright',
                leg_cont = as.character(1:4))