drawScatterplotTrack: Add a scatterplot track to an existing plot

In gmoviz: Seamless visualization of complex genomic variations in GMOs and edited cell lines

Description

Adds a scatterplot track to the existing plot. Must have initialised the circular plot (by gmovizInitialise first).

Usage

drawScatterplotTrack(plot_data, track_border_colour = "black",
  track_height = 0.3, point_bicolour_cutoff = NULL,
  point_colour = "black", point_outline_colour = "black",
  point_size = 0.55, point_type = 21, ylim = NULL,
  yaxis_increment = NULL, show_yaxis = TRUE, yaxis_label_size = 0.6,
  yaxis_tick_size = 0.5, yaxis_location = CELL_META$sector.index,
  yaxis_side = "left", yaxis_colour = "black", show_gridlines = TRUE,
  gridline_colour = "#aaaaaa")

Arguments

plot_data	Either: (1) a GRanges object with a metadata column of y values to plot OR (2) a data frame with four columns; chr (should match those supplied when initialising the plot); start and end (x values of the point: can both be the same if you only have a single x value for position) and then a fourth column of y values.
track_border_colour	Colour of the border of the plotting region.
track_height	The proportion (between 0 and 1) of the circle taken up by this track.
point_bicolour_cutoff	A numeric threshold for the colour of the points (points above/below this number will be different colours).
point_colour	The fill colour of the points. If point_bicolour_cutoff != NULL then this should be a vector with two elements.
point_outline_colour	The colour of the outline of the points. If using point_bicolour_cutoff then this should be a vector with two elements.
point_size	Size of the points.
point_type	Type (shape) of the points, same as base R.
ylim	Vector of length 2; upper and lower limits for y axis.
yaxis_increment	The increment the y axis and gridlines will use.
show_yaxis	If TRUE, a y axis will be drawn.
yaxis_label_size	Size of the labels on the y axis.
yaxis_tick_size	Size of the ticks on the y axis.
yaxis_location	Sector the y axis is drawn on.
yaxis_side	Side of the sector the y axis is on; either 'left' or 'right'.
yaxis_colour	Colour of the y axis.
show_gridlines	If TRUE then gridlines will be drawn.
gridline_colour	Colour of the gridlines.

Value

Adds a scatterplot track to existing visualisation.

See Also

gmovizInitialise, which must be used to initialise the graph before this function. Also drawLinegraphTrack for a similar function which displays data as a line graph instead.

Examples

## you must initialise first!
small_ideo <- data.frame(chr=c('region 1', 'region 2', 'region 3'),
                         start=c(0, 0, 0), end=c(10000, 12000, 10000))
gmovizInitialise(small_ideo, custom_sector_width=c(0.3, 0.3, 0.3))

## make the data
smallplot_data <- data.frame(
chr = sample(c('region 1', 'region 2','region 3'), size=40, replace=TRUE),
start = seq(0, 10000, length.out=40), end = seq(0, 10000, length.out=40),
val = rnorm(40, 2, 0.5))

## scatterplot where all points are the same colour
drawScatterplotTrack(smallplot_data)

## scatterplot with bi-colour cutoff of 2
drawScatterplotTrack(smallplot_data, point_bicolour_cutoff=2,
                     point_colour=c('red', 'blue'),
                     point_outline_colour=c('black', 'black'))

gmoviz documentation built on Nov. 8, 2020, 5:41 p.m.