clonal_count {barcodetrackR} | R Documentation |
A line plot that tracks the total number of clones or the cumulative number of clones from selected samples of the SummarizedExperiment object plotted over a specified variable.
clonal_count( your_SE, percent_threshold = 0, plot_over, plot_over_display_choices = NULL, keep_numeric = TRUE, group_by, group_by_choices = NULL, cumulative = FALSE, point_size = 3, line_size = 2, text_size = 12, your_title = NULL, return_table = FALSE )
your_SE |
Summarized Experiment object containing clonal tracking data as created by the barcodetrackR 'create_SE' function. |
percent_threshold |
Numeric. The percent threshold for which to count barcodes as present or not present. Set to 0 by default. |
plot_over |
The column of metadata that you want to be the x-axis of the plot. e.g. timepoint |
plot_over_display_choices |
Choice(s) from the column designated in plot_over that will be used for plotting. Defaults to all if left as NULL. |
keep_numeric |
If plot_over is numeric, whether to space the x-axis appropriately according to the numerical values. |
group_by |
The column of metadata you want to group by e.g. cell_type. |
group_by_choices |
Choice(s) from the column designated in group_by that will be used for plotting. Defaults to all if left as NULL. |
cumulative |
Logical. If TRUE, will plot cumulative counts over the 'plot_over' argument rather than unique counts per sample (the default, which is FALSE). |
point_size |
Numeric. Size of points. |
line_size |
Numeric. Size of lines. |
text_size |
Numeric. Size of text in plot. |
your_title |
The title for the plot. |
return_table |
Logical. If set to true, rather than returning a plot, the function will return the clonal count or cumulative count of each sample in a dataframe. |
Outputs plot of a diversity measure tracked for groups over a factor. Or if return_table is set to TRUE, a dataframe of the number of clones (or cumulative clones) for each sample.
data(wu_subset) clonal_count(your_SE = wu_subset, cumulative = FALSE, plot_over = "months", group_by = "celltype")