A function for plotting spatial phylogenetic trees on Visium 10X data.
Usage
SpatialPhyloPlot(
visium_version,
newick_file,
image_file,
tissue_positions_file,
clone_df,
scale_factors,
clone_group_column,
clone_barcode_column = "Barcode",
palette = "default",
plot_points = TRUE,
plot_polygon = FALSE,
point_alpha = 0.8,
point_size = 1.5,
point_shape = 19,
hull_alpha = 0,
hull_expansion = 0.005,
centroid_alpha = 0.9,
centroid_size = 8,
plot_internal_nodes = FALSE,
internal_node_colour = "grey80",
internal_node_size = 3,
internal_node_alpha = 0.5,
segment_alpha = 0.8,
segment_width = 2,
segment_colour = "grey",
fig_offset_x = 0,
fig_offset_y = 0,
multisample = FALSE,
shared_clones = FALSE,
plot_connections = FALSE,
image_file_left = NA,
image_file_right = NA,
image_file_top = NA,
image_file_bottom = NA,
clone_df_left = NA,
clone_df_right = NA,
clone_df_top = NA,
clone_df_bottom = NA,
tissue_positions_file_left = NA,
tissue_positions_file_right = NA,
tissue_positions_file_top = NA,
tissue_positions_file_bottom = NA,
scale_factors_left = NA,
scale_factors_right = NA,
scale_factors_top = NA,
scale_factors_bottom = NA,
connection_width = 1,
connection_colour = "grey",
nestedness = 10,
origin_coord = NA,
origin_name = "diploid",
...
)Arguments
- visium_version
Which version of Visium was used. Should be either `"V1"` or `"V2"`
- newick_file
A file path to the phylogenetic tree in the Newick format saved as a `.new` file.
- image_file
A file path to the hires Visium 10X png image to plot.
- tissue_positions_file
A file path to the Visium 10X `tissue_positions_list.csv` file for V1 or `tissue_positions.csv` file for V2.
- clone_df
A `data.frame` listing which barcode belongs to which clone.
- scale_factors
A path to the `scalefactors_json.json` file produced by SpaceRanger.
- clone_group_column
The name of the column in `clone_df` that indicates the clones.
- clone_barcode_column
The name of the column in `clone_df` that indicates the barcode.
- palette
A named list of colours for each clone. Defaults to `RColorBrewer` `Set2` followed by the `pals` `alphabet` sets.
- plot_points
Whether individual Visium spots should be plotted. Defaults to `TRUE`.
- plot_polygon
Whether a polygon should be plotted for each clone. Defaults to `FALSE`.
- point_alpha
The alpha transparency value for points, default is `0.8`.
- point_size
The size of the Visium spot points, default is `1.5`.
- point_shape
The shape to use for the Visium spot points, default is `19`.
- hull_alpha
The alpha transparency value for polygons/hulls to be plotted, default is `0` (not plotted).
- hull_expansion
The hull/polygon extension amount, default is `0.005`.
- centroid_alpha
The alpha transparency value for the centroids plotted as part of the phylogenetic tree, default is `0.9`.
- centroid_size
The size of the plotted centroid points, default is `8`.
- plot_internal_nodes
Whether or not to plot internal nodes in the tree. Defaults to `FALSE`.
- internal_node_colour
Colour used to represent internal nodes. Defaults to `"grey80"`.
- internal_node_size
Size of internal nodes. Defaults to `3`.
- internal_node_alpha
Alpha for internal nodes. Defaults to `0.5`
- segment_alpha
The alpha transparency value for phylogenetic tree segments, default is `0.8`.
- segment_width
The width of the phylogenetic tree segments, default is `2`.
- segment_colour
The colour of the phylogenetic tree segments, default is `"grey"`.
- fig_offset_x
The offset to adjust the histology image x_end location, if required. Default is `0.011`, adjustments not recommended.
- fig_offset_y
The offset to adjust the histology image y location, if required. Default is `0.011` adjustments not recommended.
- multisample
Whether multiple samples are being plotted with the same phylogenetic tree. Defaults to `FALSE`.
Whether the same clones appear in multiple samples. Defaults to `FALSE`.
- plot_connections
Whether connections should be plotted between clones that are present in multiple samples. Defaults to `FALSE`.
- image_file_left
If running in multisample mode; a file path to the hires Visium 10X png image to plot to the left of the main sample.
- image_file_right
If running in multisample mode; a file path to the hires Visium 10X png image to plot to the right of the main sample.
- image_file_top
If running in multisample mode; a file path to the hires Visium 10X png image to plot above the main sample.
- image_file_bottom
If running in multisample mode; a file path to the hires Visium 10X png image to plot below the main sample.
- clone_df_left
If running in multisample mode; a `data.frame` listing which barcode belongs to which clone belonging to the sample plotted to the left of the main sample.
- clone_df_right
If running in multisample mode; a `data.frame` listing which barcode belongs to which clone belonging to the sample plotted to the right of the main sample.
- clone_df_top
If running in multisample mode; a `data.frame` listing which barcode belongs to which clone belonging to the sample plotted above the main sample.
- clone_df_bottom
If running in multisample mode; a `data.frame` listing which barcode belongs to which clone belonging to the sample plotted below the main sample.
- tissue_positions_file_left
If running in multisample mode; a path to the Visium 10X `tissue_positions_list.csv` file for V1 or `tissue_positions.csv` file for V2, belonging to the sample plotted to the left of the main sample.
- tissue_positions_file_right
If running in multisample mode; a path to the Visium 10X `tissue_positions_list.csv` file for V1 or `tissue_positions.csv` file for V2, belonging to the sample plotted to the right of the main sample.
- tissue_positions_file_top
If running in multisample mode; a path to the Visium 10X `tissue_positions_list.csv` file for V1 or `tissue_positions.csv` file for V2, belonging to the sample plotted above the main sample.
- tissue_positions_file_bottom
If running in multisample mode; a path to the Visium 10X `tissue_positions_list.csv` file for V1 or `tissue_positions.csv` file for V2, belonging to the sample plotted below the main sample.
- scale_factors_left
If running in multisample mode; a path to the Visium 10X `scalefactors_json.json` file produced by SpaceRanger, belonging to the sample plotted to the left of the main sample.
- scale_factors_right
If running in multisample mode; a path to the Visium 10X `scalefactors_json.json` file produced by SpaceRanger, belonging to the sample plotted to the right of the main sample.
- scale_factors_bottom
If running in multisample mode; a path to the Visium 10X `scalefactors_json.json` file produced by SpaceRanger, belonging to the sample plotted below the main sample.
- connection_width
The width of the connecting segment linking clones between samples. Defaults to `1`.
- connection_colour
The colour of the connecting segment linking clones between samples. Defaults to `grey`.
- nestedness
Roughly, how many layers of internal nodes there are in the phylogenetic tree. Defaults to `10`. Consider increasing if you notice missing connections, otherwise leave as is.
- origin_coord
xy coordinates at which to plot the "origin" of the phylogenetic tree. Defaults to `NA`. Example: `c(0,1)` for top left corner.
- origin_name
Name of the origin clone in the phylogenetic tree. Defaults to `"diploid"` in line with MEDICC2 output.
- scale_factors_topIf
running in multisample mode; a path to the Visium 10X `scalefactors_json.json` file produced by SpaceRanger, belonging to the sample plotted on top of the main sample.