dist_plot: Pairwise Distance Plot

In dunbarlabNIH/barcodetrackR: Functions for Analyzing Cellular Barcoding Data

Description

Plots the pairwise distances of the specified assay between each sample-sample pair in the provided SummarizedExperiment.

Usage

dist_plot(
  your_SE,
  assay = "proportions",
  plot_labels = colnames(your_SE),
  dist_method = "euclidean",
  cluster_tree = FALSE,
  your_title = "",
  grid = TRUE,
  label_size = 10,
  plot_type = "color",
  no_negatives = FALSE,
  return_table = FALSE,
  color_pal = "Blues",
  number_size = 3,
  point_scale = 5,
  minkowski_p = 2
)

Arguments

your_SE	A Summarized Experiment object.
assay	The choice of assay to use for the correlation calculation. Set to "proportions" by default.
plot_labels	Vector of x axis labels. Defaults to colnames(your_SE).
dist_method	Character. Distance OR similarity measure from the 'proxy' package. Full list of distance and similarity measures can be found using 'summary(proxy::pr_DB)'. Default is "euclidean". Distances will be calculated for distance measures, while similarities will be calculated for similarity measures. Distance OR similarity measure will be calculated using the 'assay' specified.
cluster_tree	Logical. Whether to cluster samples and plot a hierarchical tree calculated from the distance or similarity measure used. Default is FALSE.
your_title	Character. The title for the plot.
grid	Logical. Include a grid or not in the resulting plot.
label_size	Numeric. The size of the column labels.
plot_type	Character. One of "color", "circle", or "number".
no_negatives	Logical. Whether to make negative correlations = 0.
return_table	Logical. Whether or not to return table of p-values, confidence intervals, and R values instead of displaying a plot.
color_pal	Character. One of 'Reds', 'Purples', 'Oranges', 'Greys', 'Greens', or 'Blues' that designates the brewer.pal color scale to use.
number_size	Numeric. size of the text label when plot_type is "number".
point_scale	Numeric. The size of the largest point if the plot_type is "circle".
minkowski_p	Numeric. If 'Minkowski' is chosen, the 'p' used to calculate the Minkowski distance.

Value

Plots pairwise correlation plot for the samples in your_SE.

Examples

data(wu_subset)
dist_plot(your_SE = wu_subset, plot_type = "color")
# "

dunbarlabNIH/barcodetrackR documentation built on April 26, 2021, 6:20 p.m.