R/clonalOccupy.R
clonalOccupy.Rd
View the count of clones frequency group in Seurat or SCE object
meta data after combineExpression()
. The visualization
will take the new meta data variable "cloneSize" and
plot the number of cells with each designation using a secondary
variable, like cluster. Credit to the idea goes to Drs. Carmona
and Andreatta and their work with ProjectTIL.
clonalOccupy(
sc.data,
x.axis = "ident",
label = TRUE,
facet.by = NULL,
order.by = NULL,
proportion = FALSE,
na.include = FALSE,
exportTable = FALSE,
palette = "inferno"
)
The single-cell object after combineExpression()
The variable in the meta data to graph along the x.axis.
Include the number of clone in each category by x.axis variable
The column header used for faceting the graph
A vector of specific plotting order or "alphanumeric" to plot groups in order description
Convert the stacked bars into relative proportion
Visualize NA values or not
Exports a table of the data into the global environment in addition to the visualization
Colors to use in visualization - input any hcl.pals
Stacked bar plot of counts of cells by clone frequency group
#Getting the combined contigs
combined <- combineTCR(contig_list,
samples = c("P17B", "P17L", "P18B", "P18L",
"P19B","P19L", "P20B", "P20L"))
#Getting a sample of a Seurat object
scRep_example <- get(data("scRep_example"))
#Using combineExpresion()
scRep_example <- combineExpression(combined, scRep_example)
#Using clonalOccupy
clonalOccupy(scRep_example, x.axis = "ident")
table <- clonalOccupy(scRep_example, x.axis = "ident", exportTable = TRUE)