eggplant
Getting Started:
eggplant package
About
Installation
Examples
Full Analysis Example
Landmark Lower Bound Estimation
Spatiotemporal analysis of synthetic data
eggplant
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Index
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Index
Symbols
|
_
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A
|
B
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C
|
D
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E
|
F
|
G
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H
|
I
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J
|
K
|
L
|
M
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N
|
O
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P
|
Q
|
R
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S
|
T
|
U
|
V
|
W
Symbols
**kwargs (eggplant.models.Reference.plot parameter)
*args (eggplant.models.Reference.plot parameter)
_
__init__() (eggplant.models.BaseGP method)
(eggplant.models.GPModelApprox method)
(eggplant.models.GPModelExact method)
(eggplant.models.Reference method)
A
adata (eggplant.plot.visualize_landmark_spread parameter)
(eggplant.preprocess.default_normalization parameter)
(eggplant.preprocess.get_landmark_distance parameter)
(eggplant.preprocess.match_scales parameter)
(eggplant.preprocess.spatial_smoothing parameter)
adatas (eggplant.methods.estimate_n_landmarks parameter)
(eggplant.methods.fa_transfer_to_reference parameter)
(eggplant.methods.transfer_to_reference parameter)
(eggplant.plot.visualize_observed parameter)
(eggplant.preprocess.join_adatas parameter)
add_k_in_annulus() (eggplant.methods.PoissonDiscSampler method)
alpha (eggplant.sdea.test_region_wise_enrichment parameter)
attributes (eggplant.plot.visualize_transfer parameter)
B
background (eggplant.preprocess.reference_to_grid parameter)
BaseGP (class in eggplant.models)
batch_size (eggplant.methods.fit parameter)
(eggplant.methods.transfer_to_reference parameter)
bbox_style (eggplant.plot.visualize_landmark_spread parameter)
by (eggplant.models.Reference.composite_representation parameter)
C
CCF
chart
charted
clean() (eggplant.models.Reference method)
cmap (eggplant.plot.visualize_sdea_results parameter)
col_name (eggplant.sdea.test_region_wise_enrichment parameter)
colorbar_fontsize (eggplant.plot.visualize_observed parameter)
(eggplant.plot.visualize_sdea_results parameter)
(eggplant.plot.visualize_transfer parameter)
colorbar_orientation (eggplant.plot.visualize_observed parameter)
(eggplant.plot.visualize_sdea_results parameter)
(eggplant.plot.visualize_transfer parameter)
ColorMapper (class in eggplant.plot)
compare (eggplant.sdea.get_sde_features parameter)
composite_representation() (eggplant.models.Reference method)
coord_to_cell() (eggplant.methods.PoissonDiscSampler method)
coord_type (eggplant.preprocess.spatial_smoothing parameter)
D
data (eggplant.sdea.sdea parameter)
(eggplant.sdea.test_region_wise_enrichment parameter)
default_normalization() (in module eggplant.preprocess)
device (eggplant.methods.estimate_n_landmarks parameter)
(eggplant.methods.fa_transfer_to_reference parameter)
(eggplant.methods.transfer_to_reference parameter)
(eggplant.models.BaseGP parameter)
(eggplant.models.GPModelApprox parameter)
(eggplant.models.GPModelExact parameter)
dge_res (eggplant.plot.visualize_sdea_results parameter)
diameter_multiplier (eggplant.methods.estimate_n_landmarks parameter)
(eggplant.plot.visualize_landmark_spread parameter)
display_grid (eggplant.plot.distplot_transfer parameter)
distance_key (eggplant.preprocess.spatial_smoothing parameter)
distplot_transfer() (in module eggplant.plot)
domain (eggplant.models.Reference parameter)
E
eggplant.methods
module
eggplant.models
module
eggplant.plot
module
eggplant.preprocess
module
eggplant.sdea
module
estimate_n_landmarks() (in module eggplant.methods)
exclude_highly_expressed (eggplant.preprocess.default_normalization parameter)
F
fa_transfer_to_reference() (in module eggplant.methods)
fast_computation (eggplant.methods.fit parameter)
feature (eggplant.plot.visualize_landmark_spread parameter)
(eggplant.sdea.test_region_wise_enrichment parameter)
feature_col (eggplant.sdea.test_region_wise_enrichment parameter)
feature_values (eggplant.models.BaseGP parameter)
(eggplant.models.GPModelApprox parameter)
(eggplant.models.GPModelExact parameter)
features (eggplant.methods.transfer_to_reference parameter)
(eggplant.plot.visualize_observed parameter)
fit() (in module eggplant.methods)
flip_y (eggplant.plot.visualize_observed parameter)
(eggplant.plot.visualize_transfer parameter)
fontsize (eggplant.plot.visualize_observed parameter)
(eggplant.plot.visualize_transfer parameter)
forward() (eggplant.models.GPModelApprox method)
(eggplant.models.GPModelExact method)
G
get_landmark_distance() (in module eggplant.preprocess)
get_neighbors() (eggplant.methods.PoissonDiscSampler method)
get_sde_features() (in module eggplant.sdea)
GPModelApprox (class in eggplant.models)
GPModelExact (class in eggplant.models)
group_by (eggplant.sdea.get_sde_features parameter)
group_col (eggplant.sdea.sdea parameter)
H
height (eggplant.plot.model_diagnostics parameter)
hspace (eggplant.plot.visualize_observed parameter)
(eggplant.plot.visualize_transfer parameter)
I
idx (eggplant.methods.PoissonDiscSampler.get_neighbors parameter)
include_colorbar (eggplant.plot.visualize_observed parameter)
(eggplant.plot.visualize_transfer parameter)
include_models (eggplant.sdea.test_region_wise_enrichment parameter)
include_title (eggplant.plot.visualize_observed parameter)
(eggplant.plot.visualize_transfer parameter)
inducing_points (eggplant.models.GPModelApprox parameter)
inference_method (eggplant.methods.transfer_to_reference parameter)
inside (eggplant.plot.distplot_transfer parameter)
intersect_features() (in module eggplant.preprocess)
J
join_adatas() (in module eggplant.preprocess)
joint_highly_variable_genes() (in module eggplant.preprocess)
K
k (eggplant.methods.PoissonDiscSampler.add_k_in_annulus parameter)
(eggplant.methods.PoissonDiscSampler.sample parameter)
kernel (eggplant.models.BaseGP parameter)
(eggplant.models.GPModelApprox parameter)
(eggplant.models.GPModelExact parameter)
L
label_fontsize (eggplant.plot.distplot_transfer parameter)
(eggplant.plot.visualize_landmark_spread parameter)
label_style_dict (eggplant.plot.landmark_diagnostics parameter)
labels (eggplant.sdea.get_sde_features parameter)
landmark
landmark_cmap (eggplant.plot.visualize_observed parameter)
(eggplant.plot.visualize_transfer parameter)
landmark_diagnostics() (in module eggplant.plot)
landmark_distance (eggplant.models.BaseGP parameter)
(eggplant.models.GPModelApprox parameter)
(eggplant.models.GPModelExact parameter)
landmark_lower_bound() (in module eggplant.methods)
landmark_marker_size (eggplant.plot.visualize_landmark_spread parameter)
(eggplant.plot.visualize_observed parameter)
(eggplant.plot.visualize_transfer parameter)
landmark_position_key (eggplant.preprocess.get_landmark_distance parameter)
,
[1]
landmarks
(eggplant.models.Reference parameter)
layer (eggplant.methods.estimate_n_landmarks parameter)
(eggplant.methods.fa_transfer_to_reference parameter)
(eggplant.methods.transfer_to_reference parameter)
(eggplant.plot.visualize_landmark_spread parameter)
(eggplant.plot.visualize_transfer parameter)
learn_inducing_points (eggplant.models.GPModelApprox parameter)
learning_rate (eggplant.methods.fa_transfer_to_reference parameter)
(eggplant.methods.fit parameter)
(eggplant.methods.transfer_to_reference parameter)
likelihood (eggplant.models.GPModelApprox parameter)
(eggplant.models.GPModelExact parameter)
line_style_dict (eggplant.plot.landmark_diagnostics parameter)
lmk_eval_res (eggplant.plot.landmark_diagnostics parameter)
loss_history (eggplant.models.BaseGP property)
losses (eggplant.plot.model_diagnostics parameter)
lower_bound (eggplant.plot.landmark_diagnostics parameter)
M
marker_size (eggplant.plot.visualize_landmark_spread parameter)
(eggplant.plot.visualize_observed parameter)
(eggplant.plot.visualize_sdea_results parameter)
(eggplant.plot.visualize_transfer parameter)
match_scales() (in module eggplant.preprocess)
max_cg_iterations (eggplant.methods.estimate_n_landmarks parameter)
(eggplant.methods.fa_transfer_to_reference parameter)
(eggplant.methods.transfer_to_reference parameter)
max_points (eggplant.methods.PoissonDiscSampler.sample parameter)
mean_fun (eggplant.models.BaseGP parameter)
(eggplant.models.GPModelApprox parameter)
(eggplant.models.GPModelExact parameter)
mean_marker_style (eggplant.plot.distplot_transfer parameter)
meta (eggplant.models.Reference parameter)
(eggplant.models.Reference.transfer parameter)
meta_key (eggplant.methods.fa_transfer_to_reference parameter)
(eggplant.methods.transfer_to_reference parameter)
min_cells (eggplant.preprocess.default_normalization parameter)
mixed_normal() (in module eggplant.sdea)
model (eggplant.methods.fit parameter)
model_diagnostics() (in module eggplant.plot)
models (eggplant.models.Reference.plot parameter)
(eggplant.models.Reference.transfer parameter)
(eggplant.plot.model_diagnostics parameter)
module
eggplant.methods
eggplant.models
eggplant.plot
eggplant.preprocess
eggplant.sdea
mus (eggplant.sdea.mixed_normal parameter)
N
n_approx_points (eggplant.preprocess.reference_to_grid parameter)
n_cols (eggplant.plot.distplot_transfer parameter)
(eggplant.plot.model_diagnostics parameter)
(eggplant.plot.visualize_observed parameter)
(eggplant.plot.visualize_sdea_results parameter)
(eggplant.plot.visualize_transfer parameter)
n_components (eggplant.methods.fa_transfer_to_reference parameter)
n_epochs (eggplant.methods.estimate_n_landmarks parameter)
(eggplant.methods.fa_transfer_to_reference parameter)
(eggplant.methods.fit parameter)
(eggplant.methods.transfer_to_reference parameter)
n_evals (eggplant.methods.estimate_n_landmarks parameter)
n_features (eggplant.sdea.get_sde_features parameter)
n_inducing_points (eggplant.methods.transfer_to_reference parameter)
n_max_lmks (eggplant.methods.estimate_n_landmarks parameter)
n_neigh (eggplant.preprocess.spatial_smoothing parameter)
n_permutations (eggplant.sdea.test_region_wise_enrichment parameter)
n_regions (eggplant.preprocess.reference_to_grid parameter)
n_rows (eggplant.plot.distplot_transfer parameter)
(eggplant.plot.visualize_observed parameter)
(eggplant.plot.visualize_transfer parameter)
n_std (eggplant.sdea.sdea parameter)
names (eggplant.models.Reference.transfer parameter)
no_sig_color (eggplant.plot.visualize_sdea_results parameter)
O
optimizer (eggplant.methods.fit parameter)
outside (eggplant.plot.distplot_transfer parameter)
P
plot() (eggplant.models.Reference method)
point (eggplant.methods.PoissonDiscSampler.add_k_in_annulus parameter)
(eggplant.methods.PoissonDiscSampler.coord_to_cell parameter)
PoissonDiscSampler (class in eggplant.methods)
progress_message (eggplant.methods.fit parameter)
Q
quantile_scaling (eggplant.plot.visualize_observed parameter)
(eggplant.plot.visualize_transfer parameter)
R
rate (eggplant.methods.estimate_n_landmarks parameter)
ref (eggplant.plot.distplot_transfer parameter)
(eggplant.plot.visualize_sdea_results parameter)
ref_img (eggplant.preprocess.reference_to_grid parameter)
Reference (class in eggplant.models)
reference (eggplant.methods.fa_transfer_to_reference parameter)
(eggplant.methods.transfer_to_reference parameter)
(eggplant.plot.visualize_transfer parameter)
(eggplant.preprocess.get_landmark_distance parameter)
(eggplant.preprocess.match_scales parameter)
reference_to_grid() (in module eggplant.preprocess)
region_1 (eggplant.sdea.test_region_wise_enrichment parameter)
region_2 (eggplant.sdea.test_region_wise_enrichment parameter)
reorder_axes (eggplant.plot.visualize_sdea_results parameter)
return_figures (eggplant.plot.distplot_transfer parameter)
(eggplant.plot.landmark_diagnostics parameter)
(eggplant.plot.model_diagnostics parameter)
(eggplant.plot.visualize_landmark_spread parameter)
(eggplant.plot.visualize_observed parameter)
(eggplant.plot.visualize_sdea_results parameter)
(eggplant.plot.visualize_transfer parameter)
return_losses (eggplant.methods.fa_transfer_to_reference parameter)
(eggplant.methods.transfer_to_reference parameter)
return_models (eggplant.methods.fa_transfer_to_reference parameter)
(eggplant.methods.transfer_to_reference parameter)
S
sample() (eggplant.methods.PoissonDiscSampler method)
savgol_params (eggplant.plot.landmark_diagnostics parameter)
sdea() (in module eggplant.sdea)
seed (eggplant.methods.estimate_n_landmarks parameter)
(eggplant.methods.fit parameter)
(eggplant.plot.visualize_landmark_spread parameter)
separate_colorbar (eggplant.plot.visualize_observed parameter)
(eggplant.plot.visualize_transfer parameter)
share_colorscale (eggplant.plot.visualize_observed parameter)
(eggplant.plot.visualize_transfer parameter)
show_image (eggplant.plot.visualize_observed parameter)
(eggplant.plot.visualize_transfer parameter)
show_landmarks (eggplant.plot.visualize_observed parameter)
(eggplant.plot.visualize_transfer parameter)
side_size (eggplant.plot.distplot_transfer parameter)
(eggplant.plot.landmark_diagnostics parameter)
(eggplant.plot.visualize_landmark_spread parameter)
(eggplant.plot.visualize_observed parameter)
(eggplant.plot.visualize_transfer parameter)
sigma (eggplant.preprocess.spatial_smoothing parameter)
spatial_key (eggplant.methods.estimate_n_landmarks parameter)
spatial_smoothing() (in module eggplant.preprocess)
spread_distance (eggplant.methods.estimate_n_landmarks parameter)
(eggplant.plot.visualize_landmark_spread parameter)
subsample (eggplant.methods.estimate_n_landmarks parameter)
(eggplant.methods.fa_transfer_to_reference parameter)
(eggplant.methods.transfer_to_reference parameter)
subset (eggplant.sdea.sdea parameter)
swarm_marker_style (eggplant.plot.distplot_transfer parameter)
T
tail_length (eggplant.methods.estimate_n_landmarks parameter)
test_region_wise_enrichment() (in module eggplant.sdea)
text_h_offset (eggplant.plot.visualize_landmark_spread parameter)
ticks_fontsize (eggplant.plot.distplot_transfer parameter)
ticks_style_dict (eggplant.plot.landmark_diagnostics parameter)
title_fontsize (eggplant.plot.distplot_transfer parameter)
(eggplant.plot.landmark_diagnostics parameter)
(eggplant.plot.visualize_landmark_spread parameter)
(eggplant.plot.visualize_sdea_results parameter)
total_counts (eggplant.preprocess.default_normalization parameter)
training (eggplant.models.GPModelApprox attribute)
(eggplant.models.GPModelExact attribute)
transfer() (eggplant.models.Reference method)
transfer_to_reference() (in module eggplant.methods)
U
use_highly_variable (eggplant.methods.fa_transfer_to_reference parameter)
V
variance_threshold (eggplant.methods.fa_transfer_to_reference parameter)
verbose (eggplant.methods.estimate_n_landmarks parameter)
(eggplant.methods.fa_transfer_to_reference parameter)
(eggplant.methods.fit parameter)
(eggplant.methods.transfer_to_reference parameter)
visualize_landmark_spread() (in module eggplant.plot)
visualize_observed() (in module eggplant.plot)
visualize_sdea_results() (in module eggplant.plot)
visualize_transfer() (in module eggplant.plot)
vrs (eggplant.sdea.mixed_normal parameter)
W
weights (eggplant.sdea.sdea parameter)
width (eggplant.plot.model_diagnostics parameter)
ws (eggplant.sdea.mixed_normal parameter)
wspace (eggplant.plot.visualize_observed parameter)
(eggplant.plot.visualize_transfer parameter)
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