plotting-param {cytomapper} | R Documentation

## Further plotting parameters for the cytomapper package

### Description

The `plotCells` and `plotPixels` functions share a number of parameter that can be set to change the visual representation of plotted images.

### Arguments

`missing_colour` | a single character specifying a valid colour. Cells that are not contained in the SingleCellExperiment object will be coloured based on `missing_colour`. In the `plotPixels` function, `missing_colour` defines the outline of the cells if `outline_by` is not set.
`background_colour` | (only `plotCells`) a single character specifying a valid colour that is set as the background of the image.
`scale_bar` | a list specifying features of the scale bar. One or multiple of the following entries are supported: `length`: numeric length in pixels (default 20% of the largest image width). `label`: single character specifying the scale bar label. `cex`: numeric value indicating the size of the scale bar label. `lwidth`: numeric value indicating the line width of the scale bar in pixels. By default, the line width is adjusted relative to the maximum height of the images. `colour`: single character specifying the colour of scale bar and label (default "white"). `position`: position of scale bar. Supported values: "topleft", "topright", "bottomleft", "bottomright" (default "bottomright"). `margin`: vector of two numeric entries specifying the x and y margin between image boundary and the scale bar (default c(10,10)). `frame`: either "all" to display scale bar on all images or a single number specifying the image for which the scale bar should be displayed (default "all"). Plotting of the scale bar is suppressed if set to `NULL`.
`image_title` | a list specifying features of the image titles. One or multiple of the following entries are supported: `text`: character vector of image titles. Same length as the `CytoImageList` object. `position`: single character specifying the position of the title. Supported entries: "top", "bottom", "topleft", "bottomleft", "topright", "bottomright" (default "top"). `colour`: single character specifying the colour of image title (default "white"). `margin`: vector of two numeric entries specifying the x and y margin between image boundary and the image title (default c(10,10)). `font`: numeric entry specifying the font of the image title (default 1, see `par` for details) `cex`: numeric value indicating the size of the image title. Plotting of the image title is suppressed if set to `NULL`.
`save_plot` | a list specifying how to save the plot. One or multiple of the following entries are supported: `filename`: single character specifying a valid file name. The file extension specifies the format in which the file is saved. Supported formats are: jpeg, tiff and png. If `display = "single"`, each image will be written in an individual file. The file names obtain a "_x" ending where x indicates the position of the image in the `CytoImageList` object or "legend". `scale`: by default the height and width of the saved image is defined by the maximum image size times the number of rows and number of columns. This resolution is often not sufficient to clearly display the text. The `scale` parameter can be set to increase the resolution of the image while keeping the text size constant (default 1 but can be increased for optimal results).
`return_plot` | logical indicating whether to return the plot (see `recordPlot` for more infos).
`return_images` | logical indicating whether to return the coloured images in form of a `SimpleList` object. Each entry to this list is a three-colour `Image` object. However, the image title and scale bar are not retained.
`legend` | a list specifying features of the legend. One or multiple of the following entries are supported: `colour_by.title.font`: numeric entry specifying the font of the legend title for features specified by `colour_by`. `colour_by.title.cex`: numeric entry specifying the size of the legend title for features specified by `colour_by`. `colour_by.labels.cex`: numeric entry specifying the size of the legend labels for features specified by `colour_by`. `colour_by.legend.cex`: (only discrete features) numeric entry specifying the size of the legend for features specified by `colour_by`. `outline_by.title.font`: numeric entry specifying the font of the legend title for features specified by `outline_by`. `outline_by.title.cex`: numeric entry specifying the size of the legend title for features specified by `outline_by`. `outline_by.labels.cex`: numeric entry specifying the size of the legend labels for features specified by `outline_by`. `outline_by.legend.cex`: (only discrete features) numeric entry specifying the size of the legend for features specified by `outline_by`. `margin`: numeric value indicating the margin (in pixels) between the legends and the outer boundary (default 2) Plotting of the legend is suppressed if set to `NULL`.
`margin` | numeric value indicating the gap (in pixels) between individual images (default 0).
`thick` | logical indicating whether cell borders should be drawn as thick lines (default `FALSE`).
`display` | one of two possible values: "all" or "single". When set to "all", all images are displayed at once in a grid-like fashion. When set to "single", individual images are plotted in single graphics devices. The second option is useful when saving individual images in pdf format or when displaying in Rmarkdown files.
`scale` | logical indicating whether to scale each feature individually to its minimum/maximum across the SingleCellExperiment object (see `plotCells`) or across all displayed images (see `plotCells`). If set to `FALSE` each value is displayed relative to the maximum of all selected features.
`interpolate` | a logical indicating whether to apply linear interpolation to the image when drawing (see `rasterImage`) (default TRUE).

### Value

a list if `return_images` and/or `return_plot` is TRUE.

- `plot`: a single plot object (`display = "all"`) or a list of plot objects (`display = "single"`)

- `images`: a `SimpleList` object containing three-colour `Image` objects.

### Author(s)

Nils Eling (nils.eling@dqbm.uzh.ch)

Nicolas Damond (nicolas.damond@dqbm.uzh.ch)

### See Also

`plotCells` and `plotPixels` for the main plotting functions

### Examples

    data("pancreasImages")
    data("pancreasMasks")
    data("pancreasSCE")

    # Setting missing colour
    plotCells(pancreasMasks, missing_colour = "blue")

    # Setting background colour
    plotCells(pancreasMasks, background_colour = "blue")

    # Setting the scale bar
    plotCells(pancreasMasks, scale_bar = list(length = 10,
                                            cex = 2,
                                            lwidth = 10,
                                            colour = "red",
                                            position = "bottomleft",
                                            margin = c(5,5),
                                            frame = 3))

    # Setting the image title
    plotCells(pancreasMasks,
                image_title = list(text = c("image1", "image2", "image3"),
                                    position = "topleft",
                                    colour = "blue",
                                    margin = c(0,5),
                                    font = 2,
                                    cex = 2))

    # Return plot
    cur_out <- plotPixels(pancreasImages, return_plot = TRUE)
    cur_out$plot

    # Return images
    cur_out <- plotPixels(pancreasImages, return_images = TRUE)
    cur_out$images

    # Setting the legend
    plotCells(pancreasMasks, object = pancreasSCE,
                img_id = "ImageNb", cell_id = "CellNb",
                colour_by = c("CD99", "CDH"),
                outline_by = "CellType",
                legend = list(colour_by.title.font = 0.5,
                            colour_by.title.cex = 0.5,
                            colour_by.labels.cex = 0.5,
                            outline_by.legend.cex = 0.5,
                            margin = 0))

    # Setting the margin between images
    plotPixels(pancreasImages, margin = 3)

    # Thick outlines
    plotCells(pancreasMasks, object = pancreasSCE,
                img_id = "ImageNb", cell_id = "CellNb",
                colour_by = "CD99",
                outline_by = "CellType",
                thick = TRUE)

    # Displaying individual images
    plotPixels(pancreasImages, display = "single")

    # Supress scaling
    plotPixels(pancreasImages, colour_by = c("CD99", "PIN"),
                scale = TRUE)
    plotPixels(pancreasImages, colour_by = c("CD99", "PIN"),
                scale = FALSE)

    # Suppress interpolation
    plotPixels(pancreasImages, colour_by = c("CD99", "PIN"),
                interpolate = TRUE)
    plotPixels(pancreasImages, colour_by = c("CD99", "PIN"),
                interpolate = FALSE)

[Package cytomapper version 1.4.1 Index]