AddAdjList |
Add adjacency matrix list for a PRECASTObj object |
AddParSetting |
Add model settings for a PRECASTObj object |
AddTSNE |
Add tSNE embeddings for a Seurat object |
AddUMAP |
Add UMAP embeddings for a Seurat object |
Add_embed |
Add embeddings for a Seurat object |
boxPlot |
Boxplot for a matrix |
chooseColors |
Choose color schema from a palette |
coordinate_rotate |
Coordinates rotation for visualization |
CreatePRECASTObject |
Create the PRECAST object with preprocessing step. |
dimPlot |
Low-dimensional embeddings' plot |
doHeatmap |
Heatmap for spots-by-feature matrix |
drawFigs |
Draw a figure using a group of ggplot objects |
featurePlot |
Spatial expression heatmap |
firstup |
Set the first letter of a string vector to captial |
getAdj_fixedNumber |
Calculate adjacency matrix by user-specified number of neighbors |
getAdj_reg |
Calculate adjacency matrix for regular spatial coordinates. |
Human_HK_genes |
Human housekeeping genes database |
ICM.EM |
ICM-EM algorithm implementation |
ICM.EM_structure |
ICM-EM algorithm implementation with organized paramters |
IntegrateSpaData |
Integrate multiple SRT data |
model_set |
PRECAST model setting |
Mouse_HK_genes |
Mouse housekeeping genes database |
plot_RGB |
Spatial RGB heatmap |
plot_scatter |
Scatter plot for two-dimensional embeddings |
PRECAST |
Fit a PRECAST model |
PRECASTObj |
A simple PRECASTObj for example |
PRECASTObj-class |
Each PRECASTObj object has a number of slots which store information. |
selectIntFeatures |
Select common genes for multiple data batches |
SelectModel |
Select best PRECAST model from candidated models |
SelectModel.PRECASTObj |
Select best PRECAST model from candidated models |
SelectModel.SeqK_PRECAST_Object |
Select best PRECAST model from candidated models |
SpaPlot |
Spatial heatmap |
volinPlot |
Volin/boxplot plot |