Revision f1ad799015c901dad378f6e488dc38f4a19fd703 authored by Yifang Liu on 06 November 2020, 22:49:13 UTC, committed by GitHub on 06 November 2020, 22:49:13 UTC
1 parent 404c7ab
5_2020-02-05_SoupX_output_figures.Rmd
---
title: "5 SoupX output figures for supplemental"
author: "Yifang Liu"
date: "`r Sys.Date()`"
output:
rmdformats::html_clean:
code_folding: hide
fig_width: 10
fig_height: 10
highlight: kate
thumbnails: false
lightbox: true
gallery: true
---
```{r knitr_init, echo=FALSE, cache=FALSE}
library(knitr)
library(rmdformats)
options(max.print = 200)
opts_chunk$set(echo = TRUE,
cache = FALSE,
prompt = FALSE,
tidy = TRUE,
comment = NA,
message = FALSE,
warning = FALSE,
dev = c('png', 'pdf'),
fig.width = 10,
fig.height = 10,
fig.align = "center",
fig.path = '5_PDF_2020-02-05_SoupX_output_figures/',
dpi = 72)
opts_knit$set(width = 75)
```
```{r setup}
set.seed(123)
npc <- 20
# theta1 <- 2
# theta2 <- 5
# theta <- c(theta1, theta2)
resolution <- 0.1
selected_res <- paste0("RNA_snn_res.", resolution)
pt_size <- 1
# alpha <- 0.8
# Suppress loading messages
suppressPackageStartupMessages({
library(Matrix)
library(dplyr)
library(tidyverse)
library(Seurat)
library(cowplot)
library(Rcpp)
library(harmony)
library(SoupX)
})
```
# SoupX
```{r}
fixed <- 0.45
topN <- 20
# dir.create("TSC1_EGFP_SoupX_fixed_0.45_191028")
```
# G0
## G0: Picking soup specific genes
```{r G0_tstGenes}
dataDirs <- c("/Users/yifang/Projects/With/Arpan/SoupX/TSC1_EGFP_191028/AUG27_POOL_ACG-G_SI-GA-A1")
scl <- load10X(dataDirs)
plotMarkerDistribution(scl)
```
# G1
## G1: Picking soup specific genes
```{r G1_tstGenes}
dataDirs <- c("/Users/yifang/Projects/With/Arpan/SoupX/TSC1_EGFP_191028/AUG27_POOL_ACG-G1_SI-GA-A3")
scl <- load10X(dataDirs)
plotMarkerDistribution(scl)
```
# Notes
2020-02-05:
* SoupX output figures for supplemental.
Tue Oct 29, 2019:
* Use SoupX fixed 0.45 to remove ambient RNA.
Mon Oct 7, 2019:
* Add more sequence depth.
Mon, Sep 30, 2019:
* remove genes: EGFP, Tsc1, gig. Then perform integrate analysis of EGFP, TSC1.
Fri, Sep 20, 2019:
* First version for integrate analysis of EGFP, TSC1.
# Session Info
```{r sessioninfo, message=TRUE}
sessionInfo()
```
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