plotSpillmat {CATALYST} | R Documentation |
Generates a heat map of the spillover matrix annotated with estimated spill percentages.
plotSpillmat(bc_ms, SM, ...) ## S4 method for signature 'numeric,matrix' plotSpillmat(bc_ms, SM, out_path = NULL, name_ext = NULL, annotate = TRUE, plotly = TRUE, isotope_list = NULL) ## S4 method for signature 'ANY,data.frame' plotSpillmat(bc_ms, SM, out_path = NULL, name_ext = NULL, annotate = TRUE, plotly = TRUE, isotope_list = NULL) ## S4 method for signature 'character,ANY' plotSpillmat(bc_ms, SM, out_path = NULL, name_ext = NULL, annotate = TRUE, plotly = TRUE, isotope_list = NULL)
bc_ms |
a vector of numeric masses corresponding to barcode channels. |
SM |
spillover matrix returned from |
... |
optional arguments. |
out_path |
character string. If specified, outputs will be generated here. |
name_ext |
character string. If specified, will be appended to the plot's name. |
annotate |
logical. If TRUE (default), spill percentages are shown inside bins and rows are annotated with the total amount of spill received. |
plotly |
logical. Should an interactive plot be rendered? |
isotope_list |
named list. Used to validate the input spillover matrix.
Names should be metals; list elements numeric vectors of their isotopes.
See |
Plots estimated spill percentages as a heat map. Colours are ramped to the highest spillover value present
Helena Lucia Crowell helena.crowell@uzh.ch
# get single-stained control samples data(ss_exp) # specify mass channels stained for bc_ms <- c(139, 141:156, 158:176) re <- assignPrelim(x = ss_exp, y = bc_ms) re <- estCutoffs(x = re) re <- applyCutoffs(x = re) spillMat <- computeSpillmat(x = re) plotSpillmat(bc_ms = bc_ms, SM = spillMat)