plotDeHeatmap.Rd
Takes the results from your de-analysis
and uses the expression information of your spata-object to plot a heatmap displaying
the differentially expressed genes of every cluster. Denote the feature-variable used
to generate the differential expression data.frame as input for across
.
plotDeHeatmap( object, of_sample = "", de_df, across, across_subset = NULL, n_barcode_spots = 100, verbose = TRUE, hm_colors = viridis::viridis(15), ... )
object | A valid spata-object. |
---|---|
of_sample | The sample(s) of interest specified as a single character value or vector. If set to "" (the default) the first sample is chosen. |
de_df | A data.frame containing information about differentially expressed genes. Must contain the variables:
Hint: Use the resulting data.frame of |
across | Character value. The name of the discrete feature-variable of interest. Hint: Character- or factor- variables are discrete variables. These functionally assign the barcode spots to distinct
groups or clusters (e.g. segment or seurat_clusters) whoose properties you might want
to compare against each other. Use |
across_subset | Character vector or NULL. Specify the particular groups or clusters of interest the feature-variable
specified in argument Hint: Use |
n_barcode_spots | The number of barcode-spots belonging to each cluster you want to include in the matrix. Should be lower than the total number of barcode-spots of every cluster and can be deployed in order to keep the heatmap clear and aesthetically pleasing. |
verbose | Logical. If set to TRUE informative messages regarding the computational progress will be printed. (Warning messages will always be printed.) |
hm_colors | A vector of colors to be used. |
... | Additional parameters given to |
A heatmap of class 'pheatmap'.