View source: R/spatial_visuals.R
plot_point_layer_ggplot | R Documentation |
Visualize cells in point layer according to dimension reduction coordinates
plot_point_layer_ggplot(
ggobject,
annotated_DT_selected,
annotated_DT_other,
cell_color = NULL,
color_as_factor = T,
cell_color_code = NULL,
cell_color_gradient = c("blue", "white", "red"),
gradient_midpoint = 0,
gradient_limits = NULL,
select_cell_groups = NULL,
select_cells = NULL,
point_size = 1,
point_alpha = 1,
point_border_col = "black",
point_border_stroke = 0.1,
show_cluster_center = F,
show_center_label = T,
center_point_size = 4,
center_point_border_col = "black",
center_point_border_stroke = 0.1,
label_size = 4,
label_fontface = "bold",
edge_alpha = NULL,
show_other_cells = T,
other_cell_color = "lightgrey",
other_point_size = 0.5,
show_legend = T
)
annotated_DT_selected |
annotated data.table of selected cells |
annotated_DT_other |
annotated data.table of not selected cells |
cell_color |
color for cells (see details) |
color_as_factor |
convert color column to factor |
cell_color_code |
named vector with colors |
cell_color_gradient |
vector with 3 colors for numeric data |
gradient_midpoint |
midpoint for color gradient |
gradient_limits |
vector with lower and upper limits |
select_cell_groups |
select subset of cells/clusters based on cell_color parameter |
select_cells |
select subset of cells based on cell IDs |
point_size |
size of point (cell) |
point_alpha |
transparancy of point |
point_border_col |
color of border around points |
point_border_stroke |
stroke size of border around points |
show_cluster_center |
plot center of selected clusters |
show_center_label |
plot label of selected clusters |
center_point_size |
size of center points |
label_size |
size of labels |
label_fontface |
font of labels |
edge_alpha |
column to use for alpha of the edges |
show_other_cells |
display not selected cells |
other_cell_color |
color of not selected cells |
other_point_size |
size of not selected cells |
show_legend |
show legend |
gobject |
giotto object |
Description of parameters.
ggplot
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