Plot a heatmap of CNA values.
cnaPlot(cna, limits = c(-1, 1), ratio = 0.5, cols = heatCols, x.name = "Chromosome", y.name = "Cell", legend.title = "Inferred CNA\n[log2 ratio]", x.hide = c("13", "18", "21", "Y"), orderCells = F, order.with = NULL, euclid.dist = F, angle = NULL, x.angle = NULL, y.angle = 0, axis.rel = 1, base.size = 12, axis.title.size = 12, axis.text.size = 11, base.col = "#073642", title = NULL, subtitle = NULL, caption = NULL, text.size = 12, y.hide = NULL, tile.size = 0.1, tile.col = NULL, legend.position = "right", legend.height = 2, legend.width = 0.6, legend.rel = 0.9, legend.colour = "black", legend.breaks = NULL, legend.labels = NULL, legend.justification = "top", legend.title.position = "bottom", legend.title.angle = NULL, legend.title.rel = 0.9)
| cna | matrix of CNA values (genes by cells). |
|---|---|
| limits | colour range. Cells >= upper limit will be the same colour, and likewise for cells <= lower limit. Default: c(-1, 1) |
| ratio | aspect ratio of the panel. Default: 0.7 |
| cols | character vector of colours to use. Default: heatCols |
| x.name | x axis label. Default: 'Chromosome' |
| y.name | y axis label. Default: 'Cell' |
| legend.title | PARAM_DESCRIPTION, Default: 'Inferred CNA `[log2 ratio`]' |
| x.hide | PARAM_DESCRIPTION, Default: c("13", "18", "21", "Y") |
| orderCells | boolean value indicating whether cells should be ordered by hierarchical clustering. Default: F |
| angle | angle of axes tick labels. x.angle and y.angle inherit from angle. Default: NULL |
| x.angle | angle of x axis tick labels. If left, will inherit from angle. Default: NULL |
| y.angle | angle of y axis tick labels. If left, will inherit from angle. Default: 0 |
| axis.rel | PARAM_DESCRIPTION, Default: 1 |
| base.size | PARAM_DESCRIPTION, Default: 12 |
| axis.title.size | PARAM_DESCRIPTION, Default: 12 |
| axis.text.size | PARAM_DESCRIPTION, Default: 11 |
| base.col | PARAM_DESCRIPTION, Default: '#073642' |
| title | PARAM_DESCRIPTION, Default: NULL |
| subtitle | PARAM_DESCRIPTION, Default: NULL |
| caption | PARAM_DESCRIPTION, Default: NULL |
| text.size | PARAM_DESCRIPTION, Default: 12 |
| y.hide | PARAM_DESCRIPTION, Default: NULL |
| tile.size | PARAM_DESCRIPTION, Default: 0.1 |
| tile.col | PARAM_DESCRIPTION, Default: NULL |
| legend.position | PARAM_DESCRIPTION, Default: 'right' |
| legend.height | PARAM_DESCRIPTION, Default: 2 |
| legend.width | PARAM_DESCRIPTION, Default: 0.6 |
| legend.rel | PARAM_DESCRIPTION, Default: 0.9 |
| legend.colour | PARAM_DESCRIPTION, Default: 'black' |
| legend.breaks | PARAM_DESCRIPTION, Default: NULL |
| legend.labels | PARAM_DESCRIPTION, Default: NULL |
| legend.justification | PARAM_DESCRIPTION, Default: 'top' |
| legend.title.position | PARAM_DESCRIPTION, Default: 'bottom' |
| legend.title.angle | PARAM_DESCRIPTION, Default: NULL |
| legend.title.rel | PARAM_DESCRIPTION, Default: 0.9 |
OUTPUT_DESCRIPTION
DETAILS
# NOT RUN { if(interactive()){ #EXAMPLE1 } # }