Plot tree and spots
Usage
img_plot(
raster_img,
raster_img_left,
raster_img_right,
raster_img_top,
raster_img_bottom,
coordinates_df_scaled,
coordinates_df_scaled_left,
coordinates_df_scaled_right,
coordinates_df_scaled_top,
coordinates_df_scaled_bottom,
newick_df,
newick_df_left,
newick_df_right,
newick_df_top,
newick_df_bottom,
from_to_df,
from_to_df_left,
from_to_df_right,
from_to_df_top,
from_to_df_bottom,
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,
palette,
multisample,
shared_clones,
plot_connections,
connections_coords,
connection_width,
connection_colour
)Arguments
- raster_img
The raster image object containing the tissue image to be plotted.
- raster_img_left
The raster image object containing the tissue image to be plotted to the left of the main image.
- raster_img_right
The raster image object containing the tissue image to be plotted to the right of the main image.
- raster_img_top
The raster image object containing the tissue image to be plotted above the main image.
- raster_img_bottom
The raster image object containing the tissue image to be plotted below the main image.
- coordinates_df_scaled
A `data.frame` with the scaled (0-1) spot coordinates for each Visium barcode.
- coordinates_df_scaled_left
A `data.frame` with the scaled (0-1) spot coordinates for each Visium barcode to be plotted to the left of the main tissue.
- coordinates_df_scaled_right
A `data.frame` with the scaled (0-1) spot coordinates for each Visium barcode to be plotted to the right of the main tissue.
- coordinates_df_scaled_top
A `data.frame` with the scaled (0-1) spot coordinates for each Visium barcode to be plotted above the main tissue.
- coordinates_df_scaled_bottom
A `data.frame` with the scaled (0-1) spot coordinates for each Visium barcode to be plotted below the main tissue.
- newick_df
The newick `data.frame` generated from the .new phylogenetic tree file.
- newick_df_left
The newick `data.frame` generated from the .new phylogenetic tree file with connections to plot to the left of the main tissue.
- newick_df_right
The newick `data.frame` generated from the .new phylogenetic tree file with connections to plot to the right of the main tissue.
- newick_df_top
The newick `data.frame` generated from the .new phylogenetic tree file with connections to plot above the main tissue.
- newick_df_bottom
The newick `data.frame` generated from the .new phylogenetic tree file with connections to plot below the main tissue.
- from_to_df
A `data.frame` containing the start and end coordinates of each branch on the phylogenetic tree.
- from_to_df_left
A `data.frame` containing the start and end coordinates of each branch on the phylogenetic tree to be plotted to the left of the main tissue.
- from_to_df_right
A `data.frame` containing the start and end coordinates of each branch on the phylogenetic tree to be plotted to the right of the main tissue.
- from_to_df_top
A `data.frame` containing the start and end coordinates of each branch on the phylogenetic tree to be plotted above the main tissue.
- from_to_df_bottom
A `data.frame` containing the start and end coordinates of each branch on the phylogenetic tree to be plotted below the main tissue.
- 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.
- palette
A named list of colours for each clone. Defaults to `RColorBrewer` `Set2` followed by the `pals` `alphabet` sets.
- 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`.
- connections_coords
A `data.frame` of coordinates linking clones found in multiple samples.
- 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`.