cor_plot {barcodetrackR} | R Documentation |
Plots the pairwise correlation between the specified assay of each sample-sample pair in the provided SummarizedExperiment.
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 )
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" |
Plots pairwise correlation plot for the samples in your_SE.
data(wu_subset) cor_plot(your_SE = wu_subset, plot_type = "color") # "