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Ggpicrust2FunctionalAnalysis

  • ggPicrust2 (paper can be found here) is an R package developed explicitly for PICRUSt2 predicted functional profile.
  • ggpicrust2() integrates ko abundance which is the abundance of different gene orthologs in your microbial community generated by Picrust2 to kegg pathway abundance conversion that represents the predicted abundance of entire metabolic pathways, which are composed of multiple KO groups. It also involves annotation of pathway and differential abundance (DA) analysis in order to understand the functional potential of your microbial community at the pathway level
  • It takes PICRUSt2 original output pred_metagenome_unstrat.tsv generated using Picrust2 Functional Analysis task without reformat and a metadata file.
  • The mainstream visualization of PICRUSt2 is error_bar_plot, pca_plot and heatmap_plot. pathway_errorbar can show the relative abundance difference between groups and log2 fold change and P-values (adjusted) derived from DA results in term of pathway abundance. All the p-adjusted values that you see are significantly < 0.05. pathway_pca() can show the difference after dimensional reduction via principal component analysis. pathway_heatmap() Pairwise comparison between groups in terms of pathway differential abundance.
Attributes
config_specs: ConfigSpecsinput_specs: InputSpecsmessage_dispatcher: MessageDispatcheroutput_specs: OutputSpecsstyle: TypingStyle
Functions
__init__

Constructor, please do not overwrite this method, use the init method instead Leave the constructor without parameters

build_plotly
pca_file_path : Any
pca_proportion_file_path : Any
Reference_column : Any
Return type : PlotlyResource
check_before_run

This can be overwritten to perform custom check before running task. See doc of CheckBeforeTaskResult for more information

params : ConfigParams
inputs : TaskInputs
Return type : CheckBeforeTaskResult
create_tmp_dir

Create a temporary directory. This directory will be deleted after the task is run. Output file or folder are moved out of this directory before it is deleted.

Return type : str
get_default_output_spec_type
spec_name : str
Return type : Type
get_scenario_id
Return type : str
get_task_id
Return type : str
init

This can be overwritten to perform custom initialization of the task. This method is called just after the init and before the check_before_run method

log_debug_message
message : str
log_error_message
message : str
log_info_message
message : str
log_message

Store a message in the progress

message : str
message to store in the progress
type_ : MessageLevel
log_success_message
message : str
log_warning_message
message : str
run

Run the task

params : ConfigParams
inputs : TaskInputs
Return type : Dict
run_after_task

This can be overwritten to perform action after the task run. This method is called after the resources are saved. This method is useful to delete temporary objects (like files) to clear the server after the task is run.

update_progress_value

Update the progress value

value : float
value between 0 and 100 of the progress
message : str
if provided a message is stored on the progress
classname @classmethod

Returns the name of the class

slugify : bool - False
True to slugify the class name if True
snakefy : bool - False
True to snakefy the class name if True
replace_uppercase : bool - False
Replace upper cases by "-" if True
Return type : str
full_classname @classmethod

Returns the full name of the class

slugify : bool - False
Slugify the returned class name if True
snakefy : bool - False
Snakefy the returned class name if True
Return type : str
get_brick_name @classmethod
Return type : str
get_brick_version @classmethod
Return type : Version
get_human_name @classmethod

Get the human name of the object

Return type : str
get_input_specs @classmethod

Returns the input specs of the process

Return type : InputSpecs
get_output_specs @classmethod

Returns the input specs of the process

Return type : OutputSpecs
get_short_description @classmethod

Get the short description of the object

Return type : str
get_style @classmethod

Get the style of the object

Return type : TypingStyle
get_typing_name @classmethod

Get the typing name of the object Ex: 'RESOURCE.gws_core.Table'

Return type : str
get_typing_name_obj @classmethod
Return type : TypingNameObj
inheritors @classmethod

Get all the classes that inherit this class

Return type : List