plot_metrics | R Documentation |
This function generates plots of several common metrics (total reads,
coverage) against each other for a set of libraries. It plots horizontal and vertical lines at the
standard QC thresholds for each metric. In addition, it plots lines at standard outlier thresholds, and
labels points beyond these thresholds with the library identifiers. Points are optionally colored by
values of a discrete or continuous variable from design
specified by by_var
.
Some options still need to be built in, e.g. plotting names of all libraries, modifying threshold values
for each metric, etc.
plot_metrics(
metrics,
metrics.libID_col = "lib.id",
design = NULL,
design.libID_col = "lib.id",
threshold.perc_aligned = 0.8,
column.perc_aligned = "mapped_reads_w_dups",
threshold.total_reads = 5,
column.total_reads = "pf_hq_aligned_reads",
threshold.median_cv_coverage = 1,
column.median_cv_coverage = "median_cv_coverage",
by_var = NULL,
by_var_levels = NULL,
by_var_lab = NULL,
my_cols = c("blue", "red"),
na_col = "grey50",
point_names = "thresholded",
point_size = 1,
plot_outlier_lines = TRUE,
file_prefix = NULL,
plotdims = c(9, 9)
)
metrics |
matrix or data frame containing values of metrics. Should have metrics in columns and libraries in rows. |
metrics.libID_col |
name or number of the column in |
design |
matrix or data frame containing the library information. Should have variables in columns and libraries in rows. |
design.libID_col |
name or number of the column in |
threshold.perc_aligned |
numeric, the threshold for percent of reads aligned. Libraries with values below this threshold are flagged. Defaults to 0.8. Set to NULL to remove threshold. |
column.perc_aligned |
the name or number of the column in |
threshold.total_reads |
numeric, the threshold for total reads, in millions. Libraries with values below this threshold are flagged. Defaults to 5. Set to NULL to remove threshold. |
column.total_reads |
the name or number of the column in |
threshold.median_cv_coverage |
numeric, the threshold for median CV coverage. Libraries with values above this threshold are flagged. Defaults to 1. Set to NULL to remove threshold. |
by_var |
(optional) character string or integer identifying the column in design to color points by. If not provided, points are plotted in black. |
by_var_levels |
(optional) character vector defining the order of elements in the variable used for coloring points; this order is used for the plot legend and to match the order of colors (if provided). If not provided, levels of the variable are ordered by order of appearance in the design object. |
by_var_lab |
(optional) string to be used as the title for the color legend. |
my_cols |
(optional) vector of colors to use for plotting. If |
na_col |
color to use for NA values of |
point_names |
the points to label in the plot. Defaults to "thresholded", which selects the points outside the thresholds. Can be a character vector of library IDs to plot. Set to NULL to remove all point labels. |
point_size |
numeric, the size of the points to be plotted. Defaults to 1. |
plot_outlier_lines |
logical, whether to plot the lines where points would be considered outliers, based on the Q1-1.5*IQR / Q3+1.5*IQR threshold. Defaults to TRUE. |
file_prefix |
a character string. If provided, the function outputs pdfs of the plots, named "file_prefix_plot_name.pdf". If not provided, the function prints to a plotting window. |
plotdims |
a numeric vector, the size (in inches) of the plotting object. Either the size of the pdfs, or the size of the plotting windows. |
column.median_cv |
the name or number of the column in |
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