Depending on the pipeline used to generate the single-cell object,
there may be inherent mismatches in the barcodes in the single-cell
object and the output of combineBCR()
or
combineTCR()
. In particular, by default, Seurat will amend
the suffix of the barcodes with _X, so the barcodes change like:
original: ACGTACGTACGTACGT-1
seurat-modified: ACGTACGTACGTACGT-1_1
scRepertoire uses the samples in combineTCR()
or
combineBCR()
to add a prefix to the barcodes (using the
samples and/or ID parameters):
original: ACGTACGTACGTACGT-1
scRepertoire-modified: Sample1_ACGTACGTACGTACGT-1
The easiest way to make these compatible is to rename the cell
barcodes in the Seurat object by using the RenameCells()
from the SeuratObject package.
cell.barcodes <- rownames(seuratObj[[]])
# removing the _1 at the end of the barcodes)
cell.barcodes <- stringr::str_split(cell.barcodes, "_", simplify = TRUE)[, 1]
# adding the prefix of the orig.ident to the barcodes, assuming that is the sample ids
cell.barcodes <- paste0(seuratObj$orig.ident, "_", cell.barcodes)
seuratObj <- RenameCells(seuratObj, new.names = cell.barcodes)
For all visualizations in scRepertoire, there are 2 ways to adjust the color scheme:
hcl.pals()
.
clonalQuant(combined.TCR,
cloneCall="strict",
chain = "both",
scale = TRUE,
palette = "Zissou 1")
clonalQuant(combined.TCR,
cloneCall="strict",
chain = "both",
scale = TRUE) +
scale_fill_manual(values = hcl.colors(8,"geyser"))
Within each of the general analysis functions, there is the ability to export the data frame used to create the visualization. To get the exported values, use exportTable = TRUE. It will return the data frame used to make the graph instead of the visual output.
clonalQuant_output <- clonalQuant(combined.TCR,
cloneCall="strict",
scale = TRUE,
exportTable = TRUE)
clonalQuant_output
## contigs values total scaled
## 1 745 P17B 2805 26.55971
## 2 2117 P17L 2893 73.17663
## 3 1254 P18B 1328 94.42771
## 4 1202 P18L 1278 94.05321
## 5 5544 P19B 6942 79.86171
## 6 1619 P19L 2747 58.93702
## 7 6087 P20B 8991 67.70103
## 8 192 P20L 201 95.52239
Submit a GitHub issue - if possible please include a reproducible example. Alternatively, an example with the internal scRep_example and contig_list would be extremely helpful.