get.qc.barplot {OmicsQC}

Generates the standard barplot of scores for each sample

Description

This function takes the quality score data generated by accumulate.zscores() and returns the barplot if no filename is specified. If filename is is specified it saves the plot as file and returns NULL. It will also draw a cut-off for which samples to exclude. get.qc.barplot offers a standard template for generating a QC barplot, but can also take any parameter that BoutrosLab.plotting.general::create.barplot takes for more customizability.

Usage

get.qc.barplot(
  quality.scores,
  filename = NULL,
  abline.h = -20,
  yaxis.cex = 0.8,
  xaxis.cex = 0,
  yaxis.tck = 1,
  xaxis.tck = 0,
  xlab.label = "",
  ylab.label = "Sum of Z (Z < 0)",
  ylab.cex = 1,
  abline.col = "darkgrey",
  axes.lwd = 1,
  ...
)

Arguments

quality.scores

A dataframe with columns 'Sum' (of scores) and 'Sample', i.e. the output of accumulate.zscores

filename

Filename for tiff output, or if NULL returns the trellis object itself

abline.h

Adds a horizontal line to the plot; useful for depicting the threshold for what is deemed a poor sample quality score

yaxis.cex

Size of y-axis tick labels, defaults to 0.8

xaxis.cex

Size of x-axis tick labels, defaults to 0

yaxis.tck

Specifies the length of the tick marks for y-axis, defaults to 1

xaxis.tck

Specifies the length of the tick marks for x-axis, defaults to 0

xlab.label

The label for the x-axis, defaults to ”

ylab.label

label for the y-axis, defaults to 'Sum of Z (Z < 0)'

ylab.cex

Size of y-axis label, defaults to 1

abline.col

Colour of the horizontal line on the plot, defaults to 'darkgrey'

axes.lwd

Specify line width of the axes; set to 0 to turn off axes

...

The function can also take any parameter that BoutrosLab.plotting.general::create.barplot takes

Value

The barplot or NULL depending if filename is specified