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

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