plot_nonzero: Make a ggplot graph of the number of non-zero genes by...

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

Make a ggplot graph of the number of non-zero genes by sample.

Description

This puts the number of genes with > 0 hits on the y-axis and CPM on the x-axis. Made by Ramzi Temanni <temanni at umd dot edu>.

Usage

plot_nonzero(
  data,
  design = NULL,
  colors = NULL,
  plot_labels = "repel",
  expt_names = NULL,
  max_overlaps = 5,
  label_chars = 10,
  plot_legend = FALSE,
  plot_title = NULL,
  cutoff = 0.65,
  ...
)

Arguments

data	Expt, expressionset, or dataframe.
design	Eesign matrix.
colors	Color scheme.
plot_labels	How do you want to label the graph? 'fancy' will use directlabels() to try to match the labels with the positions without overlapping anything else will just stick them on a 45' offset next to the graphed point.
expt_names	Column or character list of preferred sample names.
max_overlaps	Permit this many labels to overlap before dropping some.
label_chars	How many characters for sample names before abbreviation.
plot_legend	Print a legend for this plot?
plot_title	Add a title?
cutoff	Minimum proportion (or number) of genes below which samples might be in trouble.
...	rawr!

Value

a ggplot2 plot of the number of non-zero genes with respect to each library's CPM.

See Also

[ggplot2]

Examples

## Not run: 
 nonzero_plot <- plot_nonzero(expt = expt)

## End(Not run)

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.