Generates the standard barplot of scores for each sample
get.qc.barplot.Rd
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