View source: R/plot_saturation_curve.R
plot_saturation_curve | R Documentation |
Plot the saturation of gene detection based on rarefaction of the mapped read counts from a library.
This function takes the output of estimate_saturation
.
plot_saturation_curve(
saturation,
design,
design_id_col = "libid",
plot_points = FALSE,
color_points_by_var = NULL,
plot_lines = TRUE,
color_lines_by_var = NULL,
plot_terminal_points = TRUE,
color_terminal_points_by_var = NULL,
plot_smooths = FALSE,
color_smooths_by_var = NULL,
log_transform_depth = FALSE,
log_transform_genes = FALSE,
my_cols = NULL
)
saturation |
a data frame, typically the output of |
design |
an optional data frame containing annotation data for use in coloring points, lines, and/or smooths. Must include a column matching column "sample" in |
design_id_col |
the number or name of the column containing identifiers that match the "sample" column in |
plot_points |
logical, whether to include points in the plot. |
color_points_by_var, color_lines_by_var, color_terminal_points_by_var, color_smooth_by_var |
variable to use for plotting points, lines, terminal points, and/or smooths by a discrete variable. Must be either the name of a column in |
plot_lines |
logical, whether to include (unsmoothed) lines in the plot. It is not recommended to include both |
plot_terminal_points, |
whether to plot the maximum-depth point for each library. This helps to visualize the actual distribution of observed counts by library. |
log_transform_depth |
logical, whether to plot the read counts on a log10 scale. Defaults to FALSE. |
log_transform_genes |
logical, whether to plot the number of genes detected on a log10 scale. Defaults to FALSE. |
my_cols |
character vector of color names for use in plotting. If not specified, |
plot_smooth |
logical, whether to include lowess curves in the plot. It is not recommended to include both |
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