Make multiple plots for multiple columns and/or multiple sample/group/clusters

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.

align.xy.by

DEFAULT = dat. Align X and Y to a dataset. By default it will be based on the total dataset.

align.col.by

DEFAULT = dat. Align colour to a dataset. By default it will be based on the total dataset.

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?

add.label

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

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.

legend.loc

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

Author

Thomas Ashhurst, thomas.ashhurst@sydney.edu.au Felix Marsh-Wakefield, felix.marsh-wakefield@sydney.edu.au Givanna Putri

Examples

Spectre::make.multi.plot(dat = Spectre::demo.clustered,
                          x.axis = "UMAP_X",
                          y.axis = "UMAP_Y",
                          plot.by = c("Ly6C_asinh", "B220_asinh", "CD45_asinh"))




#> Check your working directory for a new .png called 'Multi plot.png'