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