make_heatmap | R Documentation |
This function render a Heatmap using ComplexHeatmap package.
make_heatmap(
data,
add_rowannot = "Product_Batch",
add_colannot = "Class",
log_data = FALSE,
scale_data = "column",
order_data = TRUE,
row_dend = TRUE,
row_nclust = 2,
col_dend = TRUE,
col_nclust = 3,
dist_method = "euclidean",
clust_method = "ward.D2",
col_lab = "Lipids",
unit_legend = "ug/ml",
col_label_size = 8,
padding = c(2, 2, 2, 15)
)
data |
A summarizedexperiment object. Tested only on sumexp averaged |
add_rowannot |
A column used for the left (row) annotation (e.g. "Product_Batch") |
add_colannot |
A column used for the bottom (column) annotation (e.g. "Class") |
log_data |
Logical value. Set to TRUE to perform a log2 scaling. |
scale_data |
Scaling data option. Data can be scaled (using scale()) by row ("row"), by column ("column") or not scaled ("none"). The result is the z-score. |
order_data |
Logical value. Set to TRUE if you want to performin the ordering based on the add_rowannot value. |
row_dend |
Boolean. Render dendogram on rows (TRUE or FALSE). |
row_nclust |
Numeric. Number of cluster in the row dendrogram. |
col_dend |
Boolean. Render dendogram on columns (TRUE or FALSE). |
col_nclust |
Numeric. Number of cluster in the column dendrogram. |
dist_method |
Choose a distance method (e.g "euclidean"). See ?stats::dist(). |
clust_method |
Choose a clustering method (e.g "ward.D"). See ?stats::hclust(). |
col_lab |
A label for the column (i.e. "Lipids"). |
unit_legend |
An unit label for the legend. If data are scaled will be "Z-score" otherwise will be the input. |
col_label_size |
Size of the column labels. By default col_label_size = 10. |
padding |
padding for the heatmap in mm. By default padding = c(2,2,2,15). |
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