Function reference • iSC.MEB

All functions

Addposition(): Add position information to fitted model

CalculateTSNE(): Run t-SNE dimensionality reduction.

CalculateUMAP(): Run UMAP dimensionality reduction

CreateiSCMEBObject(): Create the iSC.MEB object with preprocessing step.

CreateNeighbors(): Calculate adjacency matrix form spatial coordinates.

doDEG(): Run DEG for a Seurat object.

doHeatmap(): Heatmap for spots-by-feature matrix

embeddings(): Get the identity of iSC.MEB

fit.iscmeb(): Fit a iSC.MEB model.

Human_HK_genes: Human housekeeping genes from the Housekeeping and Reference Transcript Atlas.

idents(): Get the identity of iSC.MEB

IntegrateSpaData(): Integrate multiple SRT expression data

iSCMEB(): Fit a iSC.MEB model.

iSCMEBObj-class: Each iSCMEBObj object has a number of slots which store information.

iSCMEBObj_toy: A toy data to help user get started with our packages.

iSCMEBResObj-class: Each iSCMEBResObj object has a number of slots which store information.

LowEmbedPlot(): Plot low-dimensional embeddings

Mouse_HK_genes: Mouse housekeeping genes from the Housekeeping and Reference Transcript Atlas.

plot_RGB(): Plot spatial RGB heatmap.

plot_scatter(): Scatter plot for two-dimensional embeddings

runPCA(): Dimensionality reduction using PCA.

SelectKPlot(): SelectKPlot.

SelectModel(): Select best iSC.MEB model from candidated models.

SetModelParameters(): Set model parameters for iSC.MEB method

SpaHeatMap(): Plot spatial heatmap