Plot_filtering_overview: plot cells filtered by each filtering steps.

In BinDuan/MASCOT: Model-based Analysis of Single cell CRISPR knockOuT screening

Description

Plotting a graph to show cells filtered by all four filtering steps, including "quality control", "zeroRatio", "sgRNA efficiency" and "phenotype capture".

Usage

Plot_filtering_overview(sample_info_gene_original = c(), sample_info_gene_qc = c(), nonzeroRatio = c(), sample_info_gene_qc_zr_se = c(), sample_info_gene_qc_zr_se_pc = c(), plot_path = "~/overview_of_cell_filterings.pdf")

Arguments

sample_info_gene_original	A character vector showing the knockout gene of each sample without any filtering steps.
sample_info_gene_qc	A character vector showing the knockout gene of each sample after filtering step "quality control". It obtains from the result of "singleCellCRISPRscreen_qc"
nonzeroRatio	A dataframe showing the ratio of nonzero knockout value in control cells for each knockout. It obtains from the result of "cellFilteringAndKOefficiencyCalculating".
sample_info_gene_qc_zr_se	A character vector showing the knockout gene of each sample after filtering steps "quality control", "zeroRatio" and "sgRNA efficiency". It obtains from the result of "cellFilteringAndKOefficiencyCalculating".
sample_info_gene_qc_zr_se_pc	A character vector showing the knockout gene of each sample after filtering steps "quality control", "zeroRatio", "sgRNA efficiency" and "phenotype capture". It obtains from the result of "cellFilteringAndKOefficiencyCalculating".
plot_path	The path of the graph.

Value

A dataframe showing the cell number filtered by corresponding filtering step.

Author(s)

Bin Duan

BinDuan/MASCOT documentation built on May 23, 2019, 2:42 p.m.