Plot expression heatmap for counts dataframe

Arguments

moo_counts: counts dataframe (Required)
sample_metadata: sample metadata as a data frame or tibble (Required)
sample_id_colname: The column from the sample metadata containing the sample names. The names in this column must exactly match the names used as the sample column names of your input Counts Matrix. (Default: NULL - first column in the sample metadata will be used.)
feature_id_colname: The column from the counts dataa containing the Feature IDs (Usually Gene or Protein ID). This is usually the first column of your input Counts Matrix. Only columns of Text type from your input Counts Matrix will be available to select for this parameter. (Default: NULL - first column in the counts matrix will be used.)
group_colname: The column from the sample metadata containing the sample group information. This is usually a column showing to which experimental treatments each sample belongs (e.g. WildType, Knockout, Tumor, Normal, Before, After, etc.).
label_colname: The column from the sample metadata containing the sample labels as you wish them to appear in the plots produced by this template. This can be the same Sample Names Column. However, you may desire different labels to display on your figure (e.g. shorter labels are sometimes preferred on plots). In that case, select the column with your preferred Labels here. The selected column should contain unique names for each sample. (Default: NULL – sample_id_colname will be used.)
color_values: vector of colors as hex values or names recognized by R
samples_to_include: Which samples would you like to include? Usually, you will choose all sample columns, or you could choose to remove certain samples. Samples excluded here will be removed in this step and from further analysis downstream of this step. (Default: NULL - all sample IDs in moo@sample_meta will be used.)
include_all_genes: Set to TRUE if all genes are to be included. Set to FALSE if you want to filter genes by variance and/or provide a list of specific genes that will appear in the heatmap.
filter_top_genes_by_variance: Set to TRUE if you want to only include the top genes by variance. Set to FALSE if you do not want to filter genes by variance.
top_genes_by_variance_to_include: The number of genes to include if filtering genes by variance. This parameter is ignored if "Filter top genes by variance" is set to FALSE.
specific_genes_to_include_in_heatmap: Enter the gene symbols to be included in the heatmap, with each gene symbol separated with a space from the others. Alternatively, paste in a column of gene names from any spreadsheet application. This parameter is ignored if "Include all genes" is set to TRUE.
cluster_genes: Choose whether to cluster the rows (genes). If TRUE, rows will have clustering applied. If FALSE, clustering will not be applied to rows.
gene_distance_metric: Distance metric to be used in clustering genes. (TODO document options)
gene_clustering_method: Clustering method metric to be used in clustering samples. (TODO document options)
display_gene_dendrograms: Set to TRUE to show gene dendrograms. Set to FALSE to hide dendrograms.
display_gene_names: Set to TRUE to display gene names on the right side of the heatmap. Set to FALSE to hide gene names.
center_and_rescale_expression: Center and rescale expression for each gene across all included samples.
cluster_samples: Choose whether to cluster the columns (samples). If TRUE, columns will have clustering applied. If FALSE, clustering will not be applied to columns.
arrange_sample_columns: If TRUE, arranges columns by annotation groups. If FALSE, and "Cluster Samples" is FALSE, samples will appear in the order of input (samples to include)
order_by_gene_expression: If TRUE, set gene name below and direction for ordering
gene_to_order_columns: Gene to order columns by expression levels
gene_expression_order: Choose direction for gene order
smpl_distance_metric: Distance metric to be used in clustering samples. (TODO document options)
smpl_clustering_method: Clustering method to be used in clustering samples. (TODO document options)
display_smpl_dendrograms: Set to TRUE to show sample dendrograms. Set to FALSE to hide dendrogram.
reorder_dendrogram: If TRUE, set the order of the dendrogram (below)
reorder_dendrogram_order: Reorder the samples (columns) of the dendrogram by name, e.g. “sample2”,“sample3",“sample1".
display_sample_names: Set to TRUE if you want sample names to be displayed on the plot. Set to FALSE to hide sample names.
group_columns: Columns containing the sample groups for annotation tracks
assign_group_colors: If TRUE, set the groups assigned colors (below)
assign_color_to_sample_groups: Enter each sample to color in the format: group_name: color This parameter is ignored if "Assign Colors" is set to FALSE.
group_colors: Set group annotation colors.
heatmap_color_scheme: color scheme (TODO document options)
autoscale_heatmap_color: Set to TRUE to autoscale the heatmap colors between the maximum and minimum heatmap color parameters. If FALSE, set the heatmap colors between "Set max heatmap color" and "Set min heatmap color" (below).
set_min_heatmap_color: If Autoscale heatmap color is set to FALSE, set the minimum heatmap z-score value
set_max_heatmap_color: If Autoscale heatmap color is set to FALSE, set the maximum heatmap z-score value.
aspect_ratio: Set figure Aspect Ratio. Ratio refers to entire figure including legend. If set to Auto figure size is based on number of rows and columns form counts matrix. default - Auto
legend_font_size: Set Font size for figure legend. Default is 10.
gene_name_font_size: Font size for gene names. If you don't want gene labels to show, toggle "Display Gene Names" below to FALSE
sample_name_font_size: Font size for sample names. If you don't want to display samples names, toggle "Display sample names" (below) to FALSE
display_numbers: Setting to FALSE (default) will not display numerical value of heat on heatmap. Set to TRUE if you want to see these numbers on the plot.

Plot expression heatmap for counts dataframe

Arguments

See also