adcode |
false |
Whether to show R code. |
analyse_type |
null
<QC,DA,DS>
|
Specify analysis type. |
annotation_column |
null |
Column used for annotation; defaults to none. |
batch |
null |
Batch metadata column name for the analysis, if applicable. |
cluster_id |
"cluster_id" |
Default identifier for clusters. |
col_block |
null |
block_id’s diffcyt parameter. |
cols_design_GLMM_random |
null |
Columns used in GLMM for random effects. |
conditions |
null |
Conditions metadata column name under which the analysis is performed. |
conditions_reference |
null |
Reference condition for comparison in analyses. |
contrast |
null |
Contrast condition for analysis, each is compare to conditions_reference . |
fc |
1 |
Fold change threshold for significance. |
log_bar |
false |
Whether to use logarithmic scaling on bar plots. |
min_cells |
1 |
Minimum number of cells required per sample. |
min_samples |
null |
Minimum number of samples required for analysis. |
path |
<file path> |
Path to the data file. |
p_value |
0.05 |
P-value threshold for statistical significance. |
plot_legends |
null |
Metadata column name to add on graphs. |
project |
null |
Project description if provided. |
rds |
<.rds> |
RDS file name. |
show_parameters |
true |
Whether to show parameters in outputs. |
show_summary |
true |
Whether to display summary information tables. |
show_heatmap_on_off |
true |
Whether to show or hide the number of cells per fcs heatmaps. |
sorted |
false |
Whether data should be sorted on graph by conditions. |
transform |
false |
Whether data should be transformed on Differential analysis. |
subset_column |
null |
Column used for subsetting data, if applicable. |