Plots a heatmap of all protein abundances
Usage
prot.plot_heatmap_all(
se,
show_all = TRUE,
pal = "RdBu",
kmeans = FALSE,
k = 6,
col_limit = NA,
indicate = "condition",
clustering_distance = "euclidean",
show_row_names = FALSE,
row_font_size = 6,
col_font_size = 10,
plot = TRUE,
export = TRUE,
scale = TRUE,
show_row_dend = FALSE,
...
)Arguments
- se
A SummarizedExperiment object
- show_all
Logical. Show protein abundances of all conditions or only of those in the specified constrast(s). Default is TRUE
- pal
Character. Color palette to use. Default is "RdBu"
- kmeans
Logical. Perform kmeans clustering on protein abundances. Default is FALSE
- k
Numeric. Number of clusters to use in kmeans clustering. Default is 6
- col_limit
Numeric. Maximum intensity for the heatmap. Default is NA
- indicate
Character. Column name of the annotation to indicate in the heatmap. Default is "condition"
- clustering_distance
Character. Distance metric to use for clustering. Default is "euclidean"
- show_row_names
Logical. Show protein names on the left of the heatmap. Default is FALSE
- row_font_size
Numeric. Font size for protein names. Default is 6
- col_font_size
Numeric. Font size for condition names. Default is 10
- plot
Logical. Plot the heatmap or not. Default is TRUE
- export
Logical. Export the heatmap to a pdf and png file. Default is TRUE
- scale
Logical. Scale the data before plotting. Default is TRUE
- show_row_dend
Logical. Show row dendrogram. Default is FALSE
- ...
Other parameters to pass to ComplexHeatmap::Heatmap