plotFreqHeatmap: Plot a table of counts with colours indicating frequency

In HLindsay/CrispRVariants: Tools for counting and visualising mutations in a target location

Description

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

Usage

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

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

# Plot the frequency heatmap
plotFreqHeatmap(gol)

HLindsay/CrispRVariants documentation built on May 28, 2019, 12:40 p.m.