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

View source: R/plotSphereLogFC.R

Visualize hyperspheres in low-dimensional space, coloured by log-fold change in abundance for each hypersphere.

1 2 | ```
plotSphereLogFC(x, y, logFC, max.logFC=NULL, zero.col="grey80",
left.col="blue", right.col="red",length.out=100, pch=16, ...)
``` |

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

`logFC` |
A numeric vector of log-fold changes for each hypersphere. |

`max.logFC` |
A numeric scalar specifying the maximum absolute log-fold change. |

`zero.col` |
A string specifying the colour to use at a log-fold change of zero. |

`left.col` |
A string specifying the colour to use at the most negative log-fold change. |

`right.col` |
A string specifying the colour to use at the most positive log-fold change. |

`length.out` |
An integer scalar specifying the resolution of the colour bar. |

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

Each hypersphere is represented by a point in the two-dimensional embedding, coloured from blue (negative log-FC) to grey (zero log-FC) to red (positive log-FC).
The darkness of the grey colour is set with `zero.col`

.

If `max.logFC`

is not `NULL`

, extreme values in `logFC`

are winsorized to lie within `[-max.logFC, max.logFC]`

.
This preserves the resolution of colours for smaller log-fold changes.

A plot of the low-dimensional embedding of the hypersphere locations is made on the current graphics device.
A vector of colours of length `length.out`

is returned, containing the colour gradient used for the log-fold changes.
The vector name contains the numeric values associated with each colour.
This can be used to construct a colour bar with `createColorBar`

.

Aaron Lun

1 2 3 4 5 6 7 8 9 10 11 12 | ```
# Making up some coordinates.
x <- rnorm(100)
y <- rnorm(100)
# Log-FC plot and colour bar.
logFC <- rnorm(100)
out <- plotSphereLogFC(x, y, logFC)
out <- plotSphereLogFC(x, y, logFC, max.logFC=0.5)
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, "Log-FC", cex=1.2)
``` |

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