plotmarkergenes | R Documentation |
This functions generates a heatmap of expression for defined group of genes and can highlight the clustering partition and another sample grouping, e.g. origin or cell type.
plotmarkergenes(
object,
genes,
imputed = FALSE,
cthr = 0,
cl = NULL,
cells = NULL,
order.cells = FALSE,
aggr = FALSE,
norm = FALSE,
cap = NULL,
flo = NULL,
samples = NULL,
cluster_cols = FALSE,
cluster_rows = TRUE,
cluster_set = FALSE,
samples_col = NULL,
zsc = FALSE,
logscale = TRUE,
noise = FALSE,
fontsize = 10
)
object |
|
genes |
A vector with a group of gene names corresponding to a subset of valid row names of the |
imputed |
logical. If |
cthr |
Interger number greater or equal zero. Only clusters with |
cl |
Vector of valid cluster numbers contained in slot |
cells |
Vector of valid cell names corresponding to column names of slot |
order.cells |
logical. If |
aggr |
logical. If |
norm |
logical. If |
cap |
Numeric. Upper bound for gene expression. All values larger then |
flo |
Numeric. Lower bound for gene expression. All values smaller then |
samples |
A vector with a group of sample names for each cell in the same order as the column names of the |
cluster_cols |
logical. If |
cluster_rows |
logical. If |
cluster_set |
logical. If |
samples_col |
Vector of colors used for highlighting all samples contained in |
zsc |
logical. If |
logscale |
logical. If |
noise |
logical. If |
fontsize |
postive real number. Font size of gene name labels. Default is 10. |
Object with clustering information for rows and columns returned by the function pheatmap
from the package pheatmap.
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