Description Usage Arguments Value Examples
View source: R/plot_CoGAPS_pattern_dim.R
plot_CoGAPS_pattern_dim() plots Pmeans of a CoGAPS pattern on a dimensonality reduction plot
1 2 3 | plot_CoGAPS_pattern_dim(CoGAPS_res_set, Pattern_set, annotation,
dim_reduction, pattern_num, color_scale = c("slategray1", "red"),
facet_wrap_by = NULL)
|
CoGAPS_res_set |
a CoGAPS result set. If set to NULL, a Pmeans matrix may be supplied directly as input for the Pattern_set parameter. |
Pattern_set |
a string specifying the name of a pattern set (e.g. "nP20") in a CoGAPS_res_set. Alternatively, if CoGAPS_res_set is set to NULL, a Pmeans matrix may be supplied directly. |
annotation |
an annotation dataframe. Must contain columns with column names corresponding to values in the group_vector. |
dim_reduction |
a dataframe specifying the coordinates of a dimensionality reduction method (e.g. t-SNE, UMAP etc.). Each column should specify one dimension. Rownames should correspond to the rownames of the annotation object. Colnames will be used as axis labels. |
pattern_num |
numeric; which pattern to plot. |
facet_wrap_by |
a string specifying variable for facet_wrap; defaults to NULL. |
a ggplot object
1 2 | plot_CoGAPS_pattern_dim(CoGAPS_res_set= my_CoGAPS_res, Pattern_set="nP30", annotation=pData(cds),
dim_reduction = UMAP_proj, pattern_num = 7)
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