st.plot: Spatial Transcriptomics Plot
In estfernan/boost: Bayesian Modeling of Spatial Transcriptomics Data

st.plot

R Documentation

Spatial Transcriptomics Plot

Plot the absolute, dichotomised, or relative gene expression levels in a spatial transcriptomics (ST) dataset.

st.plot(expr, spots, gene.name = NULL, binary = FALSE, log.expr = TRUE)

`expr`	A numeric vector p of length n that denotes the absolute, dichotomised, or relative gene expression levels. Each entry is an integer value that denotes the gene count at spot i.
`spots`	An n-by-2 numeric matrix T to represent the geospatial profile, where each row indicates the spot location in the grid.
`gene.name`	An optional character string that specifies the gene name. The default is `NULL` which appends nothing to the plot title.
`binary`	A logical value that indicates if the gene expression levels are dichotomised. The default is `FALSE` to expect absolute or relative expression levels.
`log.expr`	A logical value that indicates if the gene expression levels should be plotted at log-level. The default is `TRUE` to log-transform the gene expression levels if they are not dichotomised.