plotMetaDataHeatmap

Creates heatmap for genes within aggregated clusters.

plotMetaDataHeatmap(
  gobject,
  expression_values = c("normalized", "scaled", "custom"),
  metadata_cols = NULL,
  selected_genes = 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_gene_order = NULL,
  gene_cor_method = "pearson",
  gene_cluster_method = "complete",
  gradient_color = c("blue", "white", "red"),
  gradient_midpoint = 0,
  gradient_limits = NULL,
  x_text_size = 10,
  x_text_angle = 45,
  y_text_size = 10,
  strip_text_size = 8,
  show_plot = NA,
  return_plot = NA,
  save_plot = NA,
  save_param = list(),
  default_save_name = "plotMetaDataHeatmap"
)

Arguments

gobject

giotto object

expression_values

expression values to use

metadata_cols

annotation columns found in pDataDT(gobject)

selected_genes

subset of genes 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_gene_order

custom gene order (default = NULL)

gene_cor_method

correlation method for genes

gene_cluster_method

hierarchical cluster method for the genes

gradient_color

vector with 3 colors for numeric data

gradient_midpoint

midpoint for color gradient

gradient_limits

vector with lower and upper limits

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 showSaveParameters

default_save_name

default save name

Value

ggplot or data.table

Details

Creates heatmap for the average expression of selected genes in the different annotation/cluster groups. Calculation of cluster or gene order is done on the provided expression values, but visualization is by default on the z-scores. Other options are the original values or z-scores rescaled per gene (-1 to 1).

See also

plotMetaDataCellsHeatmap for numeric cell annotation instead of gene expression.

Examples

if (FALSE) {

data(mini_giotto_single_cell)

# get all genes
all_genes = slot(mini_giotto_single_cell, 'gene_ID')

# look at cell metadata
cell_metadata = pDataDT(mini_giotto_single_cell)

# plot heatmap per cell type, a column name from cell_metadata
plotMetaDataHeatmap(mini_giotto_single_cell,
                    selected_genes = all_genes[1:10],
                    metadata_cols = 'cell_types')

}