cor_plot: Correlation Plot

Description Usage Arguments Value Examples

View source: R/cor_plot.R

Description

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

Usage

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cor_plot(
  your_SE,
  assay = "proportions",
  plot_labels = colnames(your_SE),
  method_corr = "pearson",
  your_title = "",
  grid = TRUE,
  label_size = 8,
  plot_type = "color",
  no_negatives = FALSE,
  return_table = FALSE,
  color_scale = "default",
  number_size = 3,
  point_scale = 1
)

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).

method_corr

Character. One of "pearson", "spearman", or "kendall".

your_title

Character. The title for the plot.

grid

Logical. Include a grid or not in the correlation 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_scale

Character. Either "default" or an odd-numbered color scale where the lowest value will correspond to -1, the median value to 0, and the highest value to 1.

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"

Value

Plots pairwise correlation plot for the samples in your_SE.

Examples

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

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