plot-totalCountFilt: Plot totalCountFilt Object

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

Plot totalCountFilt Object

Description

For plotting an S3 object of type 'totalCountFilt':

Usage

## S3 method for class 'totalCountFilt'
plot(
  x,
  min_count = NULL,
  interactive = FALSE,
  x_lab = NULL,
  y_lab = NULL,
  x_lab_size = 11,
  y_lab_size = 11,
  x_lab_angle = 0,
  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 totalCountFilt that contains the molecule identifier and the number of total counts for which the molecule was measured (not NA).
min_count	integer specifying the minimum number of samples in which a biomolecule must appear. 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	integer specifying the size of the text (number of biomolecules by sample) within the bar plot. The default is 3.
bar_width	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 <- total_count_filter(omicsData = rnaseq_object)
plot(seqfilt, min_count = 15)

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