Description Usage Arguments Value
Plot the clustering result of cells and genes.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 | cheatmap(
mat,
filename = NA,
vmax = 2,
vmin = -1,
log = FALSE,
scale = FALSE,
hlight = NULL,
cmap = NULL,
cluster_rows = TRUE,
cluster_cols = TRUE,
gene_labels = NULL,
cell_labels = NULL,
gene_order = NULL,
cell_order = NULL,
gaps_row = NULL,
gaps_col = NULL,
anno_row = NULL,
anno_col = NULL,
plot_gaps_row = TRUE,
plot_gaps_col = TRUE,
re_write_gene_labels = FALSE,
re_write_cell_labels = FALSE,
show_colnames = FALSE,
...
)
|
mat |
Expression matrix, columns are cells and rows are genes. |
filename |
Filename to save your heatmap. |
vmax |
The maximum value to plot. |
vmin |
The minimum value to plot. |
log |
log2 tranform the data. |
scale |
Scale the data, result in mean = 0 and std = 1 of each gene. |
hlight |
The genes you want to highlight in the heatmap. |
cmap |
The pallette of the heatmap, one can generate it using colorRampPalette(). |
cluster_rows |
boolean values determining if rows should be clustered or hclust object. |
cluster_cols |
boolean values determining if columns should be clustered or hclust object. |
gene_labels |
A vector of gene clustering labels. |
cell_labels |
A vector of cell clustering labels. |
gene_order |
Specify a sequence of gene clusters order, the values must be in gene_labels. |
cell_order |
Specify a sequence of cell clusters order, the values must be in cell_labels. |
gaps_row |
A vector indicates gaps of row, if NULL the gaps will be setting based on the gene_labels. |
gaps_col |
A vector indicates gaps of column, if NULL the gaps will be setting based on the cell_labels. |
anno_row |
Data frame that specifies the annotations shown on left side of the heatmap. Each row defines the features for a specific row. The rows in the data and in the annotation are matched using corresponding row names. Note that color schemes takes into account if variable is continuous or discrete. |
anno_col |
Similar to annotation_row, but for columns. |
plot_gaps_row |
Make gaps on row. |
plot_gaps_col |
Make gaps on column. |
re_write_gene_labels |
Re-write gene labels to an ordered sequeence. |
re_write_cell_labels |
Re-write cell labels to an ordered sequeence. |
... |
Additional arguments passed on to pheatmap. |
Ordering cluster results.
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