Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/plotSphereIntensity.R

Visualize cells or hyperspheres in low-dimensional space, coloured by marker intensities or log-fold changes.

1 2 | ```
plotSphereIntensity(x, y, intensity, irange=NULL,
col.range=viridis(100), pch=16, ...)
``` |

`x, y` |
A numeric vector of coordinates for each hypersphere. |

`intensity` |
A numeric vector specifying the marker intensities for each hypersphere. |

`irange` |
A numeric vector of length 2, specifying the upper and lower bound for the intensities. |

`col.range` |
A vector of colours specifying the colour scale to be used for increasing intensity. More values represent a higher-resolution scale. |

`pch, ...` |
Additional arguments to pass to |

Each hypersphere is represented by a point in the two-dimensional embedding, colored using the viridis colour scheme, i.e., purple (low intensity) to green (medium) to yellow (high).
If `irange`

is not `NULL`

, extreme values in `intensity`

will be winsorized to lie within `irange`

.
This preserves the resolution of colours for smaller changes at low intensities.
Users should consider using `intensityRanges`

to define appropriate values of `irange`

for each marker.

A plot of the low-dimensional embedding of the hypersphere locations is made on the current graphics device.
A vector of colours equal to `col.range`

is returned, containing the colour gradient used for the intensities.
The vector names contain the numeric values associated with each colour.
This can be used to construct a colour bar with `createColorBar`

.

Aaron Lun

`viridis`

,
`intensityRanges`

,
`createColorBar`

1 2 3 4 5 6 7 8 9 10 11 | ```
# Making up some coordinates.
x <- rnorm(100)
y <- rnorm(100)
# Intensity plot and colour bar.
intensities <- rgamma(100, 2, 2)
out <- plotSphereIntensity(x, y, intensities)
plot(0,0, type="n", axes=FALSE, ylab="", xlab="", ylim=c(-1, 1), xlim=c(-1, 0.5))
createColorBar(out)
text(-0.6, 0, srt=90, "Intensity", cex=1.2)
``` |

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