wrapper around pheatmap
pheatmap1(pmat, annotation = NULL, annotation_colors = NULL,
annotation_col = NULL, annotation_row = NULL, id_column = TRUE,
border_color = NA, clustering_callback = function(hc, ...) {
dendsort::dendsort(hc) }, clustering_distance_rows = "euclidean",
clustering_distance_cols = "euclidean", min_vals_row = 1,
min_vals_col = 1, na_col = "gray", ...)
Arguments
- pmat
- data frame to plot as matrix. can have an additional id column (if id_column == TRUE)
- annotation
- data frame with 'samp' field, and additional annotations
- annotation_colors
- tidy data frame with 3 fields: 'type' - name of the annotation, e.g. 'tissue', and pairs of 'variable' and 'color', e.g. variable='tumor', color='green'
- annotation_col
- character vector with column names from `annotation` to use to annotate columns
- annotation_row
- character vector with column names from `annotation` to use to annotate rows
- id_column
- TRUE if pmat's first column contains row ids
- border_color
- color of cell borders on heatmap, use NA if no border should be
drawn.
- clustering_callback
- callback function to modify the clustering. Is
called with two parameters: original
hclust object and the matrix
used for clustering. Must return a hclust object.
- clustering_distance_rows
- distance measure used in clustering rows. Possible
values are
"correlation" for Pearson correlation and all the distances
supported by dist, such as "euclidean", etc. If the value is none
of the above it is assumed that a distance matrix is provided.
- clustering_distance_cols
- distance measure used in clustering columns. Possible
values the same as for clustering_distance_rows.
- na_col
- specify the color of the NA cell in the matrix.
- ...
- graphical parameters for the text used in plot. Parameters passed to
grid.text, see gpar.