get.qc.heatmap {OmicsQC}

Generates the standard heatmap of scores for each sample.

Description

This function takes the the scores for each sample and each metric, after being sign-corrected, and returns the standard heatmap, if filename is NULL. If filename is not NULL it saves the heatmap to file and returns NULL. The function also takes quality.scores to make sure the samples are ordered correctly, as well as the y labels for the quality metrics. get.qc.heatmap offers a standard template for generating a QC heatmap, but can also take any parameter that BoutrosLab.plotting.general::create.barplot takes for customisability.

Usage

get.qc.heatmap(
  zscores,
  quality.scores,
  yaxis.lab = colnames(zscores),
  xaxis.lab = quality.scores[, "Sample"],
  filename = NULL,
  yaxis.cex = 0.8,
  xaxis.cex = 0,
  xlab.cex = 1,
  xlab.label = "Samples",
  clustering.method = "none",
  colour.scheme = c("red", "white"),
  colour.centering.value = 0,
  colourkey.labels.at = c(-10:0),
  colourkey.cex = 1,
  at = seq(0, -10, -2),
  same.as.matrix = TRUE,
  row.lines = seq(1, ncol(zscores), 1) + 0.5,
  grid.row = TRUE,
  row.colour = "black",
  row.lwd = 1,
  axes.lwd = 1,
  ...
)

Arguments

zscores

A dataframe of (sign-corrected) z-scores for each sample and test metric, i.e. the output of correct.zscore.signs

quality.scores

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

yaxis.lab

A vector of metric labels for the y-axis; defaults to column names of z-scores

xaxis.lab

A vector of sample labels for the x-axis; defaults to ordered Sample column elements in quality.scores

filename

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

yaxis.cex

Size of y-axis tick labels, defaults to 0.8

xaxis.cex

Size of x-axis tick labels, defaults to 0

xlab.cex

Size of x-axis label, defaults to 1

xlab.label

The label for the x-axis, defaults so 'Sample'

clustering.method

Method used to cluster the records – “none” gives unclustered data. Accepts all agglomerative clustering methods available in hclust, plus “diana” (which is divisive).

colour.scheme

Heatmap colouring. Accepts old-style themes, or a vector of either two or three colours that are gradiated to create the final palette.

colour.centering.value

What should be the center of the colour-map

colourkey.labels.at

A vector specifying the tick-positions on the colourkey

colourkey.cex

Size of colourkey label text

at

A vector specifying the breakpoints along the range of x; each interval specified by these breakpoints are assigned to a colour from the palette. Defaults to seq(0, -10, -2), to give a clear discrete display of colours. If x has values outside of the range specified by “at” those values are shown with the colours corresponding to the extreme ends of the colour spectrum and a warning is given.

same.as.matrix

Prevents the flipping of the matrix that the function normally does

row.lines

Vector specifying location of lines, default is seq(1, ncol(x), 1) + 0.5. Note: Add 0.5 to customized vector

grid.row

Allow turning off of the interior grid-lines. Default is TRUE.

row.colour

Interior grid-line colour, defaults to “black”. Can be a vector

row.lwd

Interior grid-line width, defaults to 1. Setting to zero is equivalent to grid.row = FALSE and grid.col = FALSE. Can be a vector.

axes.lwd

Width of heatmap border. Note it also changes the colourkey border and ticks

...

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

Value

The heatmap or NULL depending if filename is specified