plotFreqHeatmap {CATALYST} | R Documentation |
Heatmap of relative cluster abundances (frequencies) by sample.
plotFreqHeatmap( x, k = "meta20", m = NULL, normalize = TRUE, row_anno = TRUE, col_anno = TRUE, row_clust = TRUE, col_clust = TRUE, row_dend = TRUE, col_dend = TRUE, bars = TRUE, perc = FALSE, hm_pal = rev(brewer.pal(11, "RdBu")), k_pal = CATALYST:::.cluster_cols, m_pal = k_pal )
x |
|
k |
character string specifying the clustering to use;
valid values are |
m |
character string specifying a metaclustering
to include as an annotation when |
normalize |
logical specifying whether to Z-score normalize. |
row_anno, col_anno |
logical specifying whether to
include row/column annotations for clusters/samples;
for |
row_clust, col_clust |
logical specifying whether rows/columns (clusters/samples) should be hierarchically clustered and re-ordered accordingly. |
row_dend, col_dend |
logical specifying whether to include row/column dendrograms. |
bars |
logical specifying whether to include a barplot of cell counts per cluster as a right-hand side row annotation. |
perc |
logical specifying whether to display
percentage labels next to bars when |
hm_pal |
character vector of colors to interpolate for the heatmap. |
k_pal, m_pal |
character vector of colors
to use for cluster and merging row annotations.
If less than |
a Heatmap-class
object.
Helena L Crowell helena.crowell@uzh.ch
plotAbundances
,
plotExprHeatmap
,
plotMultiHeatmap
,
data(PBMC_fs, PBMC_panel, PBMC_md) sce <- prepData(PBMC_fs, PBMC_panel, PBMC_md) sce <- cluster(sce) # complete plotFreqHeatmap(sce, k = "meta12", m = "meta8") # minimal plotFreqHeatmap(sce, k = "meta10", normalize = FALSE, bars = FALSE, row_anno = FALSE, col_anno = FALSE, row_clust = FALSE, col_clust = FALSE) # customize colors & annotations plotFreqHeatmap(sce, k = "meta7", m = "meta4", col_anno = "condition", hm_pal = c("navy", "grey95", "gold"), k_pal = hcl.colors(7, "Set 2"), m_pal = hcl.colors(4, "Dark 3"))