warning_plot_reduced_dim_scExp {ChromSCape} | R Documentation |
A warning helper for plot_reduced_dim_scExp
warning_plot_reduced_dim_scExp( scExp, color_by, reduced_dim, downsample, transparency, size, max_distanceToTSS, annotate_clusters, min_quantile, max_quantile )
scExp |
A SingleCellExperiment Object |
color_by |
Feature used for coloration |
reduced_dim |
Reduced Dimension used for plotting |
downsample |
Number of cells to downsample |
transparency |
Alpha parameter, between 0 and 1 |
size |
Size of the points. |
max_distanceToTSS |
Numeric. Maximum distance to a gene's TSS to consider a region linked to a gene. |
annotate_clusters |
A logical indicating if clusters should be labelled. The 'cell_cluster' column should be present in metadata. |
min_quantile |
The lower threshold to remove outlier cells, as quantile of cell embeddings (between 0 and 0.5). |
max_quantile |
The upper threshold to remove outlier cells, as quantile of cell embeddings (between 0.5 and 1). |
Warning or errors if the inputs are not correct