Reference

All functions

calc_centers()

Calculate centers of spots/samples for distance based analysis

calc_diff_pairwiseSamples()

Helper function for computing pairwise differences between sample values

calc_missingness()

Calculate degree of missingness for each featurea and sample

calc_spatial_diff_ex()

Identify differentially abundant features across image

convert_to_spe()

Create a SpatialExperiment object from data

distance_based_analysis()

Identify multiomic features correlated with an distance to an image feature

enrich_gradient()

Calculate functional or pathway enrichment from a gradient

enrich_ora()

Calculate functional or pathway enrichment

impute_spe()

Impute missing values based on spatial coordinates

oneKSoilsCoords

Soil sample coordinates for the sample information

oneKSoilsMeta

Soil samples from the 1000 soils project Row names indiciate KEGG Orthologs, Column names indicate locations Soil samples metadata for the sample information

pancMeta

Here is the data to be included in the spammR package

protMeta

Protein metadata for general uniprot data, including the pancProts column for the panc data

retrieve_metaspace_data()

Retrieve data objects from metaspace

smallPancData

Pancreatic proteomics measurements from Gosline et al. proteomics study. Row names indicate individual proteins, columns indicate sample identifiers described in pancMeta. Individual values show un-transformed abundance values for each protein. List of proteomic measurements in a list sorted from individual regions of the pancreas. A subset of the data at https://figshare.com/articles/dataset/spammR_Files/29250962

spat_reduce()

Reduce a high resolution image measurement (origin) to a lower resolution measurement (target)

spatial_heatmap()

Plot data in heatmap together with image

spatial_network()

Plot network of correlated features

split_spe()

Divide SPE object into smaller objects by column features

volcano_plot()

Create a volcano plot from differential expression data