Description Usage Arguments Author(s) Examples
View source: R/make.multi.plot.R
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.
1 | 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)
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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? |
Thomas Ashhurst, thomas.ashhurst@sydney.edu.au Felix Marsh-Wakefield, felix.marsh-wakefield@sydney.edu.au
1 2 3 4 5 | # 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"))
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