plotBins {SQMtools} | R Documentation |
Barplot of the most abundant bins in a SQM object
Description
This function selects the most abundant bins across all samples in a SQM object and represents their abundances in a barplot. Alternatively, a custom set of bins can be represented.
Usage
plotBins(
SQM,
count = "percent",
N = 15,
bins = NULL,
others = TRUE,
samples = NULL,
ignore_unmapped = FALSE,
ignore_nobin = FALSE,
rescale = FALSE,
color = NULL,
base_size = 11,
max_scale_value = NULL,
metadata_groups = NULL
)
Arguments
SQM |
A SQM or a SQMlite object. |
count |
character. Either |
N |
integer Plot the |
bins |
character. Custom bins to plot. If provided, it will override |
others |
logical. Collapse the abundances of least abundant bins, and include the result in the plot (default |
samples |
character. Character vector with the names of the samples to include in the plot. Can also be used to plot the samples in a custom order. If not provided, all samples will be plotted (default |
ignore_unmapped |
logical. Don't include unmapped reads in the plot (default |
ignore_nobin |
logical. Don't include reads which are not in a bin in the plot (default |
rescale |
logical. Re-scale results to percentages (default |
color |
Vector with custom colors for the different features. If empty, we will use our own hand-picked pallete if N<=15, and the default ggplot2 palette otherwise (default |
base_size |
numeric. Base font size (default |
max_scale_value |
numeric. Maximum value to include in the y axis. By default it is handled automatically by ggplot2 (default |
metadata_groups |
list. Split the plot into groups defined by the user: list('G1' = c('sample1', sample2'), 'G2' = c('sample3', 'sample4')) default |
Value
a ggplot2 plot object.
See Also
plotBins
for plotting the most abundant bins of a SQM object; plotBars
and plotHeatmap
for plotting barplots or heatmaps with arbitrary data.
Examples
data(Hadza)
# Bins distribution.
plotBins(Hadza)