plotSpillmat {CATALYST} | R Documentation |
Generates a heatmap of the spillover matrix annotated with estimated spill percentages.
plotSpillmat( x, sm = NULL, anno = TRUE, isotope_list = CATALYST::isotope_list, hm_pal = c("white", "lightcoral", "red2", "darkred"), anno_col = "black" )
x |
|
sm |
spillover matrix to visualize. If NULL, |
anno |
logical. If TRUE (default), spill percentages are shown inside bins and rows are annotated with the total amount of spill received. |
isotope_list |
named list. Used to validate the input spillover matrix.
Names should be metals; list elements numeric vectors of their isotopes.
See |
hm_pal |
character vector of colors to interpolate. |
anno_col |
character string specifying the color to use for bin annotations. |
a ggplot2
-object showing estimated spill percentages
as a heatmap with colors ramped to the highest spillover value present.
Helena L Crowell helena.crowell@uzh.ch
# get single-stained control samples & construct SCE data(ss_exp) sce <- prepData(ss_exp) # debarcode single-positive populations bc_ms <- c(139, 141:156, 158:176) sce <- assignPrelim(sce, bc_ms, verbose = FALSE) sce <- applyCutoffs(estCutoffs(sce)) # estimate & visualize spillover matrix sce <- computeSpillmat(sce) plotSpillmat(sce)