cor_plot {barcodetrackR} | R Documentation

## Correlation Plot

### Description

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

### Usage

    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

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

[Package barcodetrackR version 1.0.0 Index]