plotExprHeatmap {CATALYST} | R Documentation |
Plots median marker expressions across samples computed on arcsinh-transformed intensities.
plotExprHeatmap( x, bin_anno = TRUE, row_anno = TRUE, palette = brewer.pal(n = 8, name = "YlGnBu"), scale = TRUE, draw_freqs = FALSE, clustering_distance = "euclidean", clustering_linkage = "average" )
x |
|
bin_anno |
logical. Specifies whether to display values inside bins. |
row_anno |
logical. Should row annotations for each factor
in |
palette |
character vector of colors to interpolate. |
scale |
logical. Should scaled values be displayed? (see details) |
draw_freqs |
logical. Should cell counts and proportions be displayed? |
clustering_distance |
character string that specifies
the metric to use in |
clustering_linkage |
character string that specifies
the linkage to use in |
Scaled values corresponds to cofactor arcsinh-transformed expression values scaled between 0 and 1 using 1 boundaries. Hierarchical clustering is performed on the unscaled data.
a HeatmapList-class
object.
Helena Lucia Crowell helena.crowell@uzh.ch
Nowicka M, Krieg C, Weber LM et al. CyTOF workflow: Differential discovery in high-throughput high-dimensional cytometry datasets. F1000Research 2017, 6:748 (doi: 10.12688/f1000research.11622.1)
data(PBMC_fs, PBMC_panel, PBMC_md) sce <- prepData(PBMC_fs, PBMC_panel, PBMC_md) plotExprHeatmap(sce, draw_freqs=TRUE)