plotMetrics {cfDNAPro} | R Documentation |
Plot the fragment size metrics (i.e. proportion, cdf and 1-cdf)
plotMetrics(x, order, plot, vline, xlim, ylim, ...)
x |
A long-format dataframe contains the metrics of different cohort. |
order |
The groups show in the final plot, the input value should be vector, e.g. ‘groups = c(’group1','group2')“, default is all folders in the folder path |
plot |
The plot type, default is 'all': both median and mean metrics will be shown. They will include: mean_prop, mean_cdf, mean_1-cdf, median_prop, median_cdf, median_1-cdf. Could also specify as "median" or "mean". |
vline |
Vertical dashed lines, default value is c(81,167). |
xlim |
The x axis range shown in the plot. Default is c(0,500). |
ylim |
The y axis range shown in the fraction of fragment size plots. Default is c(0,0.0125). |
... |
Further arguments passed to or from other methods. |
The function returns a list plots.
Haichao Wang
# Get the path to example data. path <- examplePath("groups_picard") # Calculate the metrics. df <- callMetrics(path = path) # Plot metrics. plot <- plotMetrics(df, plot = "median", order = c("cohort_1", "cohort_2") )