plot-RNAFilt: Plot RNAFilt Object

In pmartR/pmartRqc: Panomics Marketplace - Quality Control and Statistical Analysis for Panomics Data

Plot RNAFilt Object

Description

For plotting an S3 object of type 'RNAFilt'

Usage

## S3 method for class 'RNAFilt'
plot(
  x,
  plot_type = "library",
  size_library = NULL,
  min_nonzero = NULL,
  interactive = FALSE,
  x_lab = NULL,
  y_lab = NULL,
  x_lab_size = 11,
  y_lab_size = 11,
  x_lab_angle = 90,
  title_lab = NULL,
  title_lab_size = 14,
  legend_lab = "",
  legend_position = "right",
  text_size = 3,
  bar_width = 0.8,
  bw_theme = TRUE,
  palette = NULL,
  ...
)

Arguments

x	object of class RNAFilt that contains the sample identifier, library size, number of non-zero biomolecules, and proportion of non-zero biomolecules
plot_type	character string, specified as "library" or "biomolecule". "library" displays library size for each sample, "biomolecule" displays the number of unique biomolecules with non-zero counts per sample.
size_library	integer cut-off for sample library size (i.e. number of reads). Defaults to NULL.
min_nonzero	integer or float between 0 and 1. Cut-off for number of unique biomolecules with non-zero counts or as a proportion of total biomolecules. Defaults to NULL.
interactive	logical value. If TRUE produces an interactive plot.
x_lab	character string specifying the x-axis label
y_lab	character string specifying the y-axis label. The default is NULL in which case the y-axis label will be the metric selected for the metric argument.
x_lab_size	integer value indicating the font size for the x-axis. The default is 11.
y_lab_size	integer value indicating the font size for the y-axis. The default is 11.
x_lab_angle	integer value indicating the angle of x-axis labels. The default is 0.
title_lab	character string specifying the plot title
title_lab_size	integer value indicating the font size of the plot title. The default is 14.
legend_lab	character string specifying the legend title
legend_position	character string specifying the position of the legend. Can be one of "right", "left", "top", "bottom", or "none". The default is "none".
text_size	An integer specifying the size of the text (number of biomolecules by sample) within the bar plot. The default is 3.
bar_width	An integer indicating the width of the bars in the bar plot. The default is 0.8.
bw_theme	logical value. If TRUE uses the ggplot2 black and white theme.
palette	character string indicating the name of the RColorBrewer palette to use. For a list of available options see the details section in RColorBrewer.
...	further arguments passed to or from other methods.

Value

ggplot2 plot object if interactive is FALSE, or plotly plot object if interactive is TRUE

Examples

library(pmartRdata)
seqfilt <- RNA_filter(omicsData = rnaseq_object)
plot(seqfilt)

pmartR/pmartRqc documentation built on April 25, 2024, 6:18 a.m.