Description Usage Arguments Value
View source: R/visualization.R
Plot the heatmap of single cell dataset
1 2 3 4 5 6 7 8 9 10 11 | plot_heatmap(
dataset,
markers,
sort_var = c("seurat_clusters"),
n = 8,
anno_var,
anno_colors,
hm_limit = c(-2, 0, 2),
hm_colors = c("#4575b4", "white", "#d73027"),
row_font_size = 12
)
|
dataset |
A Seurat object. |
markers |
A dataframe - the dataframe generated by Or a character vector - the names of genes can be directly specified. |
sort_var |
A character vector - the variables to be sorted in the heatmap, should exist in the |
n |
An integer - number of genes to be plotted for each |
anno_var |
A character vector - the variables in the annotation, should exist in the |
anno_colors |
A list - the color specification of annotation bars. The length should be the same as For a numeric variable, the element can be the name of a sequential or divergent palette in For a categorical variable, the element can be the names of palettes in |
hm_limit |
A numeric vector - three numeric values that dictate the lowest limit, midpoint, and highest limit of the color gradient. These three values correspond to the colors specified in the |
hm_colors |
A character vector of length 3 - three colors corresponding to the lowest limit, midpoint, and highest limit specified in |
row_font_size |
An integer - the font size of row names. |
A plot.
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