Man pages for kueckelj/SPATA
A Toolbox for Spatial Gene Expression Analysis

across	across
addFeatures	Add a new feature
addGeneSet	Add a new gene set
addUmapData	Add dimensional reductions
adjustGeneSetDf	Filter gene-set data.frame
adjusting_check_dummy	This is a text dummy
all_colorpanels	Color palette names
assessTrajectoryTrends	Trajectory trend analysis
average_genes	average_genes
check_assign	Check assign input
check_atdf	Check assessed trajectory data.frame
check_color_to	Check color to
check_compiled_trajectory_df	Check compiled trajectory data.frame
check_coordinate_variables	Check coordinate variables
check_coords_df	Check coords data.frame
check_de_df	Check de data.frame
check_display	Check display input
check_feature_df	Check feature data.frame
check_features	Check feature variables input
check_genes	Check gene input
check_gene_sets	Check gene set input
check_method	Check method input
check_monocle_input	Check monocle input
check_object	Check spata object input
checkpoint	Shiny feedback messages
check_pt	Check pt input
check_sample	Check sample input
check_segment	Check segment name
check_slot_coordinates	Check spata slots
check_smooth	Check smooth input
check_spata_df	Check coordinate data.frame
check_stdf	Check summarized trajectory data.frame
check_summarized_trajectory_df	Check stdf-input
check_trajectory	Check trajectory name input
check_uniform_genes	Check uniform genes input
check_variables	Check variables
clrp	clrp
compileCellDataSet	Initiate monocle3 analysis
compileSeuratObject	Initiate Seurat analysis
createSegmentation	Spatial Segmentation
createTrajectories	Spatial Trajectories
data_counts-class	data_counts object
dim_red-class	dim_red object
discardGeneSets	Discard gene sets
examineClusterResults	Examine clustering results
examineDeResults	Examine differentially expression results
examineTrajectoryAssessment	Examine trajectory-moddeling results
filterDE	Postprocess de-results
filterTrends	Filter variables of a certain trend
findDE	Find marker genes
findMonocleClusters	Cluster sample via monocle3
getBarcodes	Obtain barcodes of a sample
getC_joinW_combo	getC_joinW_combo
getCoordinates	Obtain spatial coordinates
getDimRedData	Obtain dimensional reduction data
getExpressionMatrix	Obtain count and expression matrix
getFeatureData	Obtain feature data
getFeatureNames	Obtain feature names
getFeatureValues	Obtain unique categorical feature values
getFeatureVariables	Obtain a feature variable
getGenes	Obtain gene names
getGeneSetOverview	Overview about the current gene sets
getGeneSets	Obtain gene set names
getSegmentNames	Obtain segment names
getSpataDf	Obtain a spata-data.frame
getTrajectoryComment	Obtain a trajectory comment
getTrajectoryComment-spata-method	Obtain a trajectory comment
getTrajectoryDf	Obtain a summarized trajectory data.frame
getTrajectoryNames	Obtain trajectory names
getTrajectoryObject	Obtain trajectory object
gsdf	The default collection of frequently used gene-sets
hlpr_add_models	Helper functions for trajectory ranking
hlpr_assess_trajectory_trends	Assess trajectory ranking.
hlpr_assign	Assign objects into the global environment
hlpr_compare_samples	Compare samples within an object
hlpr_compile_trajectory	Compiles a trajectory data.frame
hlpr_gene_set_name	Removes the class part of a gene set string
hlpr_image_add_on	Provides the image as ggplot background
hlpr_labs_add_on	Return customized ggplot:labs()
hlpr_normalize_imap	Normalize gene or gene set values
hlpr_normalize_vctr	Normalize gene or gene set values
hlpr_one_distinct	Number of distinct values equal to 1?
hlpr_rank_trajectory_trends	Rank trajectory trends.
hlpr_smooth	Smooth variables spatially
hlpr_smooth_shiny	Smooth variable spatially in mini-shiny-apps
hlpr_subset_across	Subset the across-variables
hlpr_summarize_trajectory_df	Join and summarize compiled trajectory data.frames
hlpr_vector_projection	Perform vector projection
hlpr_widen_trajectory_df	Widen trajectory data.frame
image	Generics to extract a slots content
image_dummy	image_dummy
image-spata-method	Methods
initiateSpataObject_10X	Initiate a spata-object
joinWith	Join barcodes with additional variables
lazy_check_dummy	lazy_check_dummy
loadSpataObject	Load and save a spata-object
moduleAddGeneSetsServer	Server of the add gene sets module
moduleAddGeneSetsUI	UI of the add gene sets module
moduleSurfacePlotServer	Server of the surface plot module
moduleSurfacePlotUI	UI of the surface plot module
normalize	normalize
pheatmap	de_df
plotDeHeatmap	Plot differentially expressed genes
plotDistribution	Distribution of continuous values
plotDistributionAcross	Distribution of continuous values
plotDistributionDiscrete	Distribution of discrete features
plot_family	plot_family
plotFourStates	Gene set state plot
plotPseudotime	Monocle3 Pseudotime
plotSegmentation	Plot segmentation
plotSurface	Plot the sample
plotSurfaceComparison	Plot several surface plots at the same time
plotTrajectory	Plot trajectory
plotTrajectoryFeatures	Trajectory line plots
plotTrajectoryFit	Display trajectory fit
plotTrajectoryHeatmap	Expression dynamic in heatmap
plotUMAP	Plot dimensional reduction
saveGeneSetDf	Save a gene set data.frame
scale_color_add_on	ggplot2 - color add on
spata-class	spata object
spata_version	The current spata-version
spatial_trajectory-class	spatial_trajectory object
subsetSpataObject	Subset a spata-object
tab_create_segmentation_return	Segmentation plot tab - return
tab_create_trajectories_return	Trajectory plot tab - return
tab_surface_plots_app	Surface plot tab - classic
tab_surface_plots_return	Surface plot tab - return
trajectory_patterns	Trajectory patterns
validateSpataObject	Validate a spata object
validation	Validate object input
variable	variable
variables_num	variables_num
verbose	verbose