plot.RNAFilt {pmartR}

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)