colored_dots: colored_dots I submitted this and it was pulled into...

In chasemc/IDBacApp: MALDI-TOF MS Protien and Small Molecule Analysis

colored_dots I submitted this and it was pulled into dendextend but is left here for less dependency/more control

Description

colored_dots I submitted this and it was pulled into dendextend but is left here for less dependency/more control

Usage

colored_dots(
  colors,
  dend,
  rowLabels = NULL,
  cex.rowLabels = 0.9,
  add = TRUE,
  y_scale,
  y_shift,
  text_shift = 1,
  sort_by_labels_order = TRUE,
  horiz = FALSE,
  circ = FALSE,
  dot_size = 1,
  ...
)

Arguments

colors	Coloring of the dots beside the dendrogram. Either a vector (one color per object) or a matrix (can also be an array or a data frame) with each column giving one group with color per object. Each column will be plotted as a colored point (when horiz = FALSE) under the dendrogram. As long as the sort_by_labels_order paramter is TRUE (default), the colors vector/matrix should be provided in the order of the original data order (and it will be re-ordered automatically to the order of the dendrogram)
dend	a dendrogram object. If missing, the colors are plotted without and re-ordering (this assumes that the colors are already ordered based on the dend's labels) This is also important in order to get the correct height/location of the colored dots (i.e.: adjusting the y_scale and y_shift)
rowLabels	Labels for the colorings given in colors. The labels will be printed to the left of the color rows in the plot. If the argument is given, it must be a vector of length equal to the number of columns in colors. If not given, names(colors) will be used if available. If not, sequential numbers starting from 1 will be used.
cex.rowLabels	Font size scale factor for the row labels. See par.
add	logical(TRUE), should the colored dots be added to an existing dendrogram plot?
y_scale	how much should the dots be stretched on the y axis? If no dend is supplied - the default will be 1
y_shift	where should the dots be plotted underneath the x axis? By default it will try to locate the dots underneath the labels (it may miss, in which case you would need to enter a number manually) If no dend is supplied - the default will be 0
text_shift	a dendrogram object
sort_by_labels_order	logical(TRUE) - if TRUE (default), then the order of the colored dots will be sorted based on the order needed to change the original order of the observations to the current order of the labels in the dendrogram. If FALSE the colored dots are plotted as-is, based on the order of the colors vector.
horiz	logical (FALSE by default). Set to TRUE when using plot(dend, horiz = TRUE)
circ	circularize, T/F
dot_size	dot_size
...	ignored at this point.

Value

NA

chasemc/IDBacApp documentation built on Oct. 22, 2022, 2:52 a.m.