makeQCPlot: Plots sequencing statistics scatterplot

In microbiomeExplorer: Microbiome Exploration App

Description

This function makes a scatterplot of read and feature counts for each sample. It was adjusted based on original work by Mo Huang

Usage

makeQCPlot(
  MRobj,
  col_by = NULL,
  log = "none",
  filter_feat = 0,
  filter_read = 0,
  allowWebGL = TRUE,
  pwidth = 550,
  pheight = 550
)

Arguments

MRobj	metagenomeSeq object to be plotted
col_by	factor by which to color the points
log	character indicating which (if any) axes should be shown as log
filter_feat	Numeric Y-coordinate to draw horizontal dashed line to indicate feature filtering. If 0 (default), no line is drawn.
filter_read	Numeric X-coordinate to draw vertical dashed line to indicate read count filtering. If 0 (default), no line is drawn.
allowWebGL	boolean indicating if webGL should be added
pwidth	overall plot width; default is 550 (125 are added for legend)
pheight	overall plot height; default is 550

Value

the plotly QC plot

Author(s)

Janina Reeder

Examples

data("mouseData", package = "metagenomeSeq")
makeQCPlot(mouseData)

microbiomeExplorer documentation built on Nov. 8, 2020, 8:16 p.m.