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Make colour plot

Source: R/make.colour.plot.R
make.colour.plot.Rd

Create a dot plot (e.g., UMAP or tSNE) of cells, coloured by a continuous variable (e.g., marker expression) or a factor (e.g., cluster, group).

Usage

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

Arguments

dat

A data.table containing the data to plot.

x.axis

Character. Column name for the x-axis.

y.axis

Character. Column name for the y-axis.

col.axis

Character or NULL. Column name for colouring points. If NULL, points are coloured by density.

col.type

Character. "continuous" (default) or "factor". Determines how col.axis is interpreted.

add.label

Logical. If TRUE and col.type = "factor", adds labels at the centroid of each group.

hex

Logical. If TRUE, uses hex binning (only for continuous colour plots).

hex.bins

Integer. Number of hex bins if hex = TRUE.

colours

Character. Colour scheme for continuous plots. Options available are: "jet", all options in RColorBrewer::brewer.pal.info, and all options in viridis pallete. Default is "spectral".

col.min.threshold

Numeric. Minimum quantile for colour scale (continuous).

col.max.threshold

Numeric. Maximum quantile for colour scale (continuous).

align.xy.by

data.table. Data to use for aligning x/y axis limits.

align.col.by

data.table. Data to use for aligning colour scale limits.

regression.line

Character or NULL. If not NULL, adds a regression line ("lm", "loess", etc.).

title

Character or NULL. Plot title. Defaults to col.axis.

filename

Character or NULL. File name for saving the plot. If NULL, a name is generated automatically.

dot.size

Numeric. Size of points.

plot.width

Numeric. Width of saved plot (in inches).

plot.height

Numeric. Height of saved plot (in inches).

nudge_x,

nudge_y Numeric. Amount to nudge centroid labels (if add.label = TRUE).

square

Logical. If TRUE, enforces a square aspect ratio.

legend.loc

Character. Legend position: "right" (default), "bottom", "top", "left", or "none".

save.to.disk

Logical. If TRUE (default), saves the plot to disk. If FALSE, only displays the plot.

path

Character. Directory to save the plot.

blank.axis

Logical. If TRUE, produces a minimalist plot with no axis lines or labels.

fast

Logical. If TRUE, uses scattermore for faster plotting of large datasets. Note, this will reduce the resolution of the plot. This only works when col.axis is specified and when hex = FALSE.

Value

A ggplot2 object representing the plot.

Author

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

Examples

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