make.colour.plot: Create a dot plot (X vs Y) coloured by a selected continuous...
In ImmuneDynamics/Spectre: High-dimensional cytometry and imaging analysis

make.colour.plot

R Documentation

Create a dot plot (X vs Y) coloured by a selected continuous (e.g. marker expression) or factorial (e..g. cluster, group) column.

Description

This function allows you to create a coloured XY plot where each cell is coloured by a selected column. Typically used to plot cells on tSNE1/2 or UMAP1/2 coloured by select cellular markers or clusters, samples, groups etc.

Usage

make.colour.plot(dat, x.axis, y.axis, col.axis)

Arguments

`dat`	NO DEFAULT. data.table Input sample.
`x.axis`	NO DEFAULT. Character. Column for X axis.
`y.axis`	NO DEFAULT. Character. Column for Y axis.
`col.axis`	DEFAULT = NULL. If not specified, plot is coloured by density. If you provide a character name of a column (e.g. "BV605.Ly6C", "Group", "FlowSOM_metacluster" etc), then each point will be coloured by the value in that column.
`col.type`	DEFAULT = "continuous". Can also be "factor".
`add.label`	DEFAULT = FALSE. Adds labels on the plot at the centroid of each factor. Only works if col.type = "factor".
`hex`	DEFAULT = FALSE. Whether to split the data into bins and show the average expression of the bin.
`hex.bins`	DEFAULT = 30. Number of bins to split into. Only used if hex is TRUE.
`colours`	DEFAULT = "spectral". Only used if type = 'colour', ignored if type = 'factor'. Specify a colour scheme. Can be "jet", "spectral", "viridis", "inferno", "magma", or "BuPu".
`col.min.threshold`	DEFAULT = 0.01. Numeric. Define minimum threshold for colour scale. Values below this limit will be coloured as the chosen minimum threshold.
`col.max.threshold`	DEFAULT = 0.995 Numeric. Define maximum threshold for colour scale. Values above this limit will be coloured as the chosen maximum threshold.
`align.xy.by`	DEFAULT = dat. data.table Sample to use to determine minimum and maximum X and Y axis values.
`align.col.by`	DEFAULT = dat. data.table. Sample to use to determine minimum and maximum colour values.
`title`	DEFAULT = col.axis. Character. Title for the plot.
`dot.size`	DEFAULT = 1. Numeric. Size of the dots.
`plot.width`	DEFAULT = 9. Width of the ggplot when saved to disk.
`plot.height`	DEFAULT = 7. Height of the ggplot when saved to disk.
`nudge_x`	DEFAULT = 0.5. When add.label = TRUE, distance the label is shifted from the centroid point on the X axis.
`nudge_y`	DEFAULT = 0.5. When add.label = TRUE, distance the label is shifted from the centroid point on the Y axis.
`square`	DEFAULT = TRUE. Ensures the plot is saved as a square. Set to FALSE if you want a plot with different X and Y lengths.
`legend.loc`	DEFAULT = 'right'. By default plot legends will be on the right hand side. Can specify the legend location to "bottom" if desired, or 'none' to remove it entirely.
`save.to.disk`	DEFAULT = TRUE. Will save the ggplot to disk. If FALSE, will only show the ggplot.
`path`	DEFAULT = getwd(). The location to save your ggplot. By default, will save to current working directory. Can be overidden.
`blank.axis`	DEFAULT = FALSE Logical, do you want a minimalist graph?

Author(s)

Thomas M Ashhurst, thomas.ashhurst@sydney.edu.au Givanna Putri

References

https://sydneycytometry.org.au/spectre

Examples

# Draw plot
Spectre::make.colour.plot(dat = Spectre::demo.clustered,
                          x.axis = "UMAP_X",
                          y.axis = "UMAP_Y",
                          col.axis = "CD4_asinh")

ImmuneDynamics/Spectre documentation built on Oct. 12, 2024, 7:55 p.m.