plot_multiple_branches_heatmap2 | R Documentation |
Create a heatmap to demonstrate the bifurcation of gene expression along multiple branches
plot_multiple_branches_heatmap2(
cds = NULL,
branches,
branches_name = NULL,
cluster_rows = TRUE,
hclust_method = "ward.D2",
num_clusters = 6,
hmcols = NULL,
add_annotation_row = NULL,
add_annotation_col = NULL,
show_rownames = FALSE,
use_gene_short_name = TRUE,
norm_method = c("vstExprs", "log"),
scale_max = 3,
scale_min = -3,
trend_formula = "~sm.ns(Pseudotime, df=3)",
return_heatmap = FALSE,
cores = 1
)
cds |
CellDataSet for the experiment (normally only the branching genes detected with BEAM) |
branches |
The terminal branches (states) on the developmental tree you want to investigate. |
branches_name |
Name (for example, cell type) of branches you believe the cells on the branches are associated with. |
cluster_rows |
Whether to cluster the rows of the heatmap. |
hclust_method |
The method used by pheatmap to perform hirearchical clustering of the rows. |
num_clusters |
Number of clusters for the heatmap of branch genes |
hmcols |
The color scheme for drawing the heatmap. |
add_annotation_row |
Additional annotations to show for each row in the heatmap. Must be a dataframe with one row for each row in the fData table of cds_subset, with matching IDs. |
add_annotation_col |
Additional annotations to show for each column in the heatmap. Must be a dataframe with one row for each cell in the pData table of cds_subset, with matching IDs. |
show_rownames |
Whether to show the names for each row in the table. |
use_gene_short_name |
Whether to use the short names for each row. If FALSE, uses row IDs from the fData table. |
norm_method |
Determines how to transform expression values prior to rendering |
scale_max |
The maximum value (in standard deviations) to show in the heatmap. Values larger than this are set to the max. |
scale_min |
The minimum value (in standard deviations) to show in the heatmap. Values smaller than this are set to the min. |
trend_formula |
A formula string specifying the model used in fitting the spline curve for each gene/feature. |
return_heatmap |
Whether to return the pheatmap object to the user. |
cores |
Number of cores to use when smoothing the expression curves shown in the heatmap. |
A list of heatmap_matrix (expression matrix for the branch committment), ph (pheatmap heatmap object), annotation_row (annotation data.frame for the row), annotation_col (annotation data.frame for the column).
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