drawScatterplotTrack {gmoviz} | R Documentation |
Adds a scatterplot track to the existing plot. Must have
initialised the circular plot (by gmovizInitialise
first).
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")
plot_data |
Either: (1) a GRanges object with a metadata
column of y values to plot OR (2) a data frame with four columns; |
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_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 |
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 |
yaxis_colour |
Colour of the y axis. |
show_gridlines |
If |
gridline_colour |
Colour of the gridlines. |
Adds a scatterplot track to existing visualisation.
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.
## 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'))