Creates heatmap for numeric cell metadata within aggregated clusters.
Usage
plotMetaDataCellsHeatmap(
gobject,
spat_unit = NULL,
feat_type = NULL,
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",
gradient_color = NULL,
gradient_midpoint = 0,
gradient_style = c("divergent", "sequential"),
midpoint = deprecated(),
x_text_size = 8,
x_text_angle = 45,
y_text_size = 8,
strip_text_size = 8,
show_plot = NULL,
return_plot = NULL,
save_plot = NULL,
save_param = list(),
default_save_name = "plotMetaDataCellsHeatmap"
)Arguments
- gobject
giotto object
- spat_unit
spatial unit (e.g. "cell")
- feat_type
feature type (e.g. "rna", "dna", "protein")
- 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 (e.g. "zscores", "original", "zscores_rescaled")
- custom_cluster_order
custom cluster order (default = NULL)
- clus_cor_method
correlation method for clusters, default to "pearson"
- clus_cluster_method
hierarchical cluster method for the clusters, default to "complete"
- custom_values_order
custom values order (default = NULL)
- values_cor_method
correlation method for values, default to "pearson"
- values_cluster_method
hierarchical cluster method for the values, default to "complete"
- gradient_color
character. continuous colors to use. palette to use or vector of colors to use (minimum of 2).
- gradient_midpoint
numeric. midpoint for color gradient
- gradient_style
either 'divergent' (midpoint is used in color scaling) or 'sequential' (scaled based on data range)
- midpoint
deprecated. Use gradient_midpoint.
- 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
logical. show plot
- return_plot
logical. return ggplot object
- save_plot
logical. save the plot
- save_param
list of saving parameters, see
showSaveParameters- default_save_name
default save name for saving, don't change, change save_name in save_param
Details
Creates heatmap for the average values of selected value columns in the different annotation groups.
See also
plotMetaDataHeatmap for feature expression instead
of numeric cell annotation data.