barcode_ggheatmap {barcodetrackR} | R Documentation |
Creates a heatmap displaying the log abundance of the top 'n' clones from each sample in the Summarized Experiment object, using ggplot2. Clones are on the y-axis and samples are on the x-axis. The ordering and clustering of clones on the y-axis as well as all aesthetics of the plot can be controlled through the arguments described below.
barcode_ggheatmap( your_SE, plot_labels = NULL, n_clones = 10, cellnote_assay = "stars", your_title = NULL, grid = TRUE, label_size = 12, dendro = FALSE, cellnote_size = 4, distance_method = "Euclidean", minkowski_power = 2, hclust_linkage = "complete", row_order = "hierarchical", clusters = 0, percent_scale = c(0, 2.5e-05, 0.001, 0.01, 0.1, 1), color_scale = c("#4575B4", "#4575B4", "lightblue", "#fefeb9", "#D73027", "red4"), return_table = FALSE )
your_SE |
A Summarized Experiment object. |
plot_labels |
Vector of x axis labels. Defaults to colnames(your_SE). |
n_clones |
The top 'n' clones to plot. |
cellnote_assay |
Character. One of "stars", "counts", or "proportions." To have no cellnote, set cellnote_size to 0. |
your_title |
The title for the plot. |
grid |
Logical. Include a grid or not in the heatmap. |
label_size |
The size of the column labels. |
dendro |
Logical. Whether or not to show row dendrogram when hierarchical clustering. |
cellnote_size |
The numerical size of the cell note labels. To have no cellnote, set cellnote_size to 0. |
distance_method |
Character. Use summary(proxy::pr_DB) to see all possible options for distance metrics in clustering. |
minkowski_power |
The power of the Minkowski distance (if minkowski is the distance method used). |
hclust_linkage |
Character. One of "ward.D", "ward.D2", "single", "complete", "average" (= UPGMA), "mcquitty" (= WPGMA), "median" (= WPGMC) or "centroid" (= UPGMC). |
row_order |
Character; "hierarchical" to perform hierarchical clustering on the output and order in that manner, "emergence" to organize rows by order of presence in data (from left to right), or a character vector of rows within the summarized experiment to plot. |
clusters |
How many clusters to cut hierarchical tree into for display when row_order is "hierarchical". |
percent_scale |
A numeric vector through which to spread the color scale (values inclusive from 0 to 1). Must be same length as color_scale. |
color_scale |
A character vector which indicates the colors of the color scale. Must be same length as percent_scale. |
return_table |
Logical. Whether or not to return table of barcode sequences with their log abundance in the 'value' column and cellnote for each sample instead of displaying a plot. |
Displays a heatmap in the current plot window. Or if return_table is set to TRUE, returns a dataframe of the barcode sequences, log abundances, and cellnotes for each sample.
data(wu_subset) barcode_ggheatmap( your_SE = wu_subset, n_clones = 10, grid = TRUE, label_size = 6 )