make.multi.plot: Make multiple plots for multiple columns and/or multiple...

In sydneycytometry/Spectre: A computational toolkit in R for the integration, exploration, and analysis of high-dimensional single-cell cytometry data.

Description

Method to create multiple plots for each marker. This function allows you to create a grid of plots, where the cells are plotted by a series of columns, and/or subsetted by a certain factor (e.g. one sample per plot). Makes use of Spectre functions make.colour.plot and make.density.plot.

Usage

make.multi.plot(dat, x.axis, y.axis, plot.by, divide.by, add.density, col.type, figure.title, align.xy.by, align.col.by, colours, dot.size, col.min.threshold, col.max.threshold, path, plot.width, plot.height, blank.axis, save.each.plot)

Arguments

dat	NO DEFAULT. A data frame containing all the data you wish to plot
x.axis	NO DEFAULT. X axis
y.axis	NO DEFAULT. Y axis
plot.by	NO DEFAULT. A vector of character names for the columns you wish to plot.
divide.by	DEFAULT = NULL. Here you can specify a character name of a column you wish to use to divide up the dataset.
add.density	DEFAULT = FALSE. Can specify to add a density plot at the end the series of colour plots
hex	DEFAULT = FALSE. Whether to split the data into bins and show the average expression of the bin. Currently does not work with density plots, only for those features in the plot.by.
hex.bins	DEFAULT = 30. Number of bins to split into. Only used if hex is TRUE.
col.type	DEFAULT = "continuous". Can also be "factor".
figure.title	DEFAULT = "Multi plot". Also used as the prefix for the saved file name.
global.xy	DEFAULT = TRUE. Defines the limits for the X and Y based on the whole dataset. If FALSE, then each plot X & Y limits scale individually.
global.col	DEFAULT = TRUE. Defines the limits for the colour axis based on the whole dataset. If FALSE, then each plot colour limit scales individually.
colours	DEFAULTS to 'spectral'. What colour scheme do you want to use. Only used if type = 'colour', ignored if type = 'factor'. Can be 'jet', 'spectral', 'viridis', 'inferno', 'magma', or "BuPu".
dot.size	DEFAULT = 1. Numeric. Size of the dots.
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.
path	DEFAULT = getwd() – i.e. the current working directory. Path to the desired output directory
plot.width	DEFAULT = 9.
plot.height	DEFAULT = 7.
blank.axis	DEFAULT = FALSE. Logical. Do you want a minimalist graph?
save.each.plot	DEFAULT = FALSE. Logical. Do you want to save each plot?

Author(s)

Thomas Ashhurst, [e-mail] Felix Marsh-Wakefield, [e-mail]

Examples

# Create grid of plots on demonstration data
Spectre::make.multi.plot(dat = as.data.table(Spectre::demo.umap),
                          x.axis = "UMAP_42_X",
                          y.axis = "UMAP_42_Y",
                          plot.by = c("BV605.Ly6C", "BUV737.B220", "AF700.CD45"))

sydneycytometry/Spectre documentation built on March 20, 2021, 2:15 a.m.