Please use make.multi.plot(fast = TRUE) instead.
Usage
fast.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?
Details
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 fast.colour.plot and make.density.plot.
Author
Thomas Ashhurst, thomas.ashhurst@sydney.edu.au Felix Marsh-Wakefield, felix.marsh-wakefield@sydney.edu.au
Examples
# Create grid of plots on demonstration data
Spectre::fast.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"))
#> Warning: `fast.multi.plot()` was deprecated in Spectre 1.3.0.
#> ℹ fast.multi.plot() will be removed in the next version. Please use
#> make.multi.plot(fast = TRUE) instead.
#> Loading required package: ggplot2
#> Loading required package: colorRamps
#> Loading required package: ggthemes
#> Loading required package: ggpointdensity
#> Loading required package: scattermore
#> Error: 'demo.umap' is not an exported object from 'namespace:Spectre'