pmartR (version 2.4.6)

plot.RNAFilt: Plot RNAFilt Object

Description

For plotting an S3 object of type 'RNAFilt'

Usage

# S3 method for 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,
  ...
)

Value

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

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.

Examples

if (FALSE) { # requireNamespace("pmartRdata", quietly = TRUE)
library(pmartRdata)
seqfilt <- RNA_filter(omicsData = rnaseq_object)
plot(seqfilt)
}