plotFreqHeatmap: Plot a table of counts with colours indicating frequency

Description Usage Arguments Value Examples

Description

Creates a heatmap from a matrix of counts or proportions, where tiles are coloured by the proportion and labeled with the value.

Usage

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plotFreqHeatmap(obj, ...)

## S4 method for signature 'matrix'
plotFreqHeatmap(obj, ..., col.sums = NULL, header = NA,
  header.name = "Total", group = NULL, group.colours = NULL,
  as.percent = TRUE, x.axis.title = NULL, x.size = 6, y.size = 8,
  x.angle = 90, legend.text.size = 6, plot.text.size = 3,
  line.width = 1, x.hjust = 1, legend.position = "right",
  x.labels = NULL, legend.key.height = grid::unit(1, "lines"))

## S4 method for signature 'CrisprSet'
plotFreqHeatmap(obj, ..., top.n = 50, min.freq = 0,
  min.count = 1, type = c("counts", "proportions"), order = NULL,
  alleles = NULL)

Arguments

obj

A matrix of counts with rows = feature, columns = sample

...

additional arguments

col.sums

Alternative column sums to be used for calculating the tile colours if as.percent = TRUE, e.g. if "obj" is a subset of a larger data set. If "NULL" (default), the column sums of "obj" are used.

header

Alternative column titles, e.g. column sums for the unfiltered data set when obj is a subset. If set to "NA", column sums of obj are displayed. If "NULL", no header is displayed (Default: NA).

header.name

Label for the header row (Default: "Total")

group

Grouping factor for columns. If supplied, columns are ordered to match the levels (Default: NULL)

group.colours

Colours for column groups, should match levels of "group". If "NULL", groups are coloured differently (Default: NULL)

as.percent

Should colours represent the percentage of reads per sample (TRUE) or the actual counts (FALSE)? (Default: TRUE)

x.axis.title

A title for the x-axis. (Default: NULL)

x.size

Font size for x-labels (Default: 16)

y.size

Font size for y-labels (Default: 16)

x.angle

Angle for x-labels (Default: 90, i.e. vertical)

legend.text.size

Font size for legend (Default: 16)

plot.text.size

Font size counts within plot (Default: 3)

line.width

Line thickness of title box'

x.hjust

Horizontal justification of x axis labels (Default: 1)

legend.position

The position of the legend (Default: right)

x.labels

X-axis labels (Default: NULL, column.names of the matrix, doesn't do anything at the moment)

legend.key.height

The height of the legend key, as a "unit" object. (See unit).

top.n

Show the n top ranked variants. Note that if the nth and n+1th variants have equal rank, they will not be shown. (Default: 50)

min.freq

i ( one sample (Default: 0, i.e no frequency cutoff)

min.count

i (integer) only plot variants with count >= i in at least one sample (default: 0, i.e no count cutoff)

type

Plot either "counts" or "proportions"

order

A list of column names or indices specifying the order of the columns in the plot

alleles

A list of alleles to include. Can be used to display only alleles of interest or to order the alleles. The default value NULL means all alleles passing the frequency cut offs will be included.

Value

The ggplot2 plot of the variant frequencies

Examples

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#Load a CrisprSet object for plotting
data("gol_clutch1")

# Plot the frequency heatmap
plotFreqHeatmap(gol)

CrispRVariants documentation built on Nov. 1, 2018, 2:20 a.m.