dimFeatPlot2D#
Last Updated: Oct 02, 2023
Description#
Visualize gene expression according to dimension reduction coordinates
Usage#
dimFeatPlot2D(
gobject,
spat_unit = NULL,
feat_type = NULL,
expression_values = c("normalized", "scaled", "custom"),
feats = NULL,
dim_reduction_to_use = "umap",
dim_reduction_name = NULL,
dim1_to_use = 1,
dim2_to_use = 2,
show_NN_network = F,
nn_network_to_use = "sNN",
network_name = "sNN.pca",
network_color = "lightgray",
edge_alpha = NULL,
scale_alpha_with_expression = FALSE,
point_shape = c("border", "no_border"),
point_size = 1,
point_alpha = 1,
cell_color_gradient = c("blue", "white", "red"),
gradient_midpoint = NULL,
gradient_limits = NULL,
point_border_col = "black",
point_border_stroke = 0.1,
show_legend = T,
legend_text = 10,
background_color = "white",
axis_text = 8,
axis_title = 8,
cow_n_col = NULL,
cow_rel_h = 1,
cow_rel_w = 1,
cow_align = "h",
show_plot = NA,
return_plot = NA,
save_plot = NA,
save_param = list(),
default_save_name = "dimFeatPlot2D"
)
Arguments#
|
giotto object |
|
spatial unit |
|
feature type |
|
gene expression values to use |
|
features to show |
|
dimension reduction to use |
|
dimension reduction name |
|
dimension to use on x-axis |
|
dimension to use on y-axis |
|
show underlying NN network |
|
type of NN network to use (kNN vs sNN) |
|
name of NN network to use, if show_NN_network = TRUE |
|
color of NN network |
|
column to use for alpha of the edges |
|
scale expression with ggplot alpha parameter |
|
point with border or not (border or no_border) |
|
size of point (cell) |
|
transparancy of points |
|
vector with 3 colors for numeric data |
|
midpoint for color gradient |
|
vector with lower and upper limits |
|
color of border around points |
|
stroke size of border around points |
|
show legend |
|
size of legend text |
|
color of plot background |
|
size of axis text |
|
size of axis title |
|
cowplot param: how many columns |
|
cowplot param: relative height |
|
cowplot param: relative width |
|
cowplot param: how to align |
|
show plots |
|
return ggplot object |
|
directly save the plot [boolean] |
|
list of saving parameters, see
|
|
default save name for saving, don’t change, change save_name in save_param |
Details#
Description of parameters.
Value#
ggplot