Creates heatmap for numeric cell metadata within aggregated clusters.
plotMetaDataCellsHeatmap( gobject, metadata_cols = NULL, spat_enr_names = NULL, value_cols = NULL, first_meta_col = NULL, second_meta_col = NULL, show_values = c("zscores", "original", "zscores_rescaled"), custom_cluster_order = NULL, clus_cor_method = "pearson", clus_cluster_method = "complete", custom_values_order = NULL, values_cor_method = "pearson", values_cluster_method = "complete", midpoint = 0, x_text_size = 8, x_text_angle = 45, y_text_size = 8, strip_text_size = 8, show_plot = NA, return_plot = NA, save_plot = NA, save_param = list(), default_save_name = "plotMetaDataCellsHeatmap" )
| gobject | giotto object |
|---|---|
| metadata_cols | annotation columns found in pDataDT(gobject) |
| spat_enr_names | spatial enrichment results to include |
| value_cols | value columns to use |
| first_meta_col | if more than 1 metadata column, select the x-axis factor |
| second_meta_col | if more than 1 metadata column, select the facetting factor |
| show_values | which values to show on heatmap |
| custom_cluster_order | custom cluster order (default = NULL) |
| clus_cor_method | correlation method for clusters |
| clus_cluster_method | hierarchical cluster method for the clusters |
| custom_values_order | custom values order (default = NULL) |
| values_cor_method | correlation method for values |
| values_cluster_method | hierarchical cluster method for the values |
| midpoint | midpoint of show_values |
| x_text_size | size of x-axis text |
| x_text_angle | angle of x-axis text |
| y_text_size | size of y-axis text |
| strip_text_size | size of strip text |
| show_plot | show plot |
| return_plot | return ggplot object |
| save_plot | directly save the plot [boolean] |
| save_param | list of saving parameters, see |
| default_save_name | default save name for saving, don't change, change save_name in save_param |
ggplot or data.table
Creates heatmap for the average values of selected value columns in the different annotation groups.
plotMetaDataHeatmap for gene expression instead of numeric cell annotation data.