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
6_2020-02-05_miniViolin_plots_of_known_marker_genes_for_all_clusters.Rmd
---
title: "6 miniViolin plots of known marker genes for all clusters"
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$set(echo = TRUE,
cache = FALSE,
prompt = FALSE,
tidy = TRUE,
comment = NA,
message = FALSE,
warning = FALSE,
dev = c("png", "pdf"),
fig.width = 10,
fig.height = 10,
fig.align = "center",
fig.path = "6_PDF_2020-02-05_miniViolin_plots_of_known_marker_genes_for_all_clusters/",
dpi = 72)
opts_knit$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)
})
```
```{r load_data}
EGFP <- readRDS("Data/2020-02-05_EGFP_seurat_obj.Rds")
Idents(EGFP) <- selected_res
```
# Markers Set1
```{r}
gene_list <- c(
"LpR1",
"FASN3",
# "Ten-a",
"salm",
# "Lsd-2",
"nmo",
"AkhR",
"daw",
"mdy",
"Pkn",
"luna",
"CG5151",
"Mhc"
# "MP2P"
)
```
# miniViolin
```{r miniViolin_set1}
for (gene in gene_list) {
plot <- VlnPlot(EGFP, features = gene, pt.size = 0, combine = FALSE)
p <- plot[[1]] +
theme(legend.position = 'none') +
theme(axis.title.x=element_blank(),
axis.text.x=element_blank(),
axis.ticks.x=element_blank()) +
ylab(gene) +
theme(plot.title = element_blank()) +
theme(axis.text.y = element_text(size = 3)) +
theme(text = element_text(size = 8))
assign(gene, p)
}
plot <- VlnPlot(EGFP, features = "Ten-a", pt.size = 0, combine = FALSE)
Tena <- plot[[1]] +
theme(legend.position = 'none') +
theme(axis.title.x=element_blank(),
axis.text.x=element_blank(),
axis.ticks.x=element_blank()) +
ylab("Ten-a") +
theme(plot.title = element_blank()) +
theme(axis.text.y = element_text(size = 3)) +
theme(text = element_text(size = 8))
plot <- VlnPlot(EGFP, features = "Lsd-2", pt.size = 0, combine = FALSE)
Lsd2 <- plot[[1]] +
theme(legend.position = 'none') +
theme(axis.title.x=element_blank(),
axis.text.x=element_blank(),
axis.ticks.x=element_blank()) +
ylab("Lsd-2") +
theme(plot.title = element_blank()) +
theme(axis.text.y = element_text(size = 3)) +
theme(text = element_text(size = 8))
x_label <- plot[[1]] +
theme(legend.position = 'none') +
ylab("") +
theme(plot.title = element_blank()) +
theme(axis.text.y = element_text(size = 3)) +
theme(text = element_text(size = 8)) +
theme(axis.text.x = element_text(size = 20))
plot_grid(
LpR1,
FASN3,
Tena,
salm,
Lsd2,
nmo,
AkhR,
daw,
mdy,
Pkn,
luna,
CG5151,
Mhc,
# MP2P,
x_label, ncol = 1)
```
# Markers Set2
```{r}
gene_list <- c(
"Mhc",
"Mp20",
"Act87E",
"Act57B",
"Mef2",
"Cyp4g1",
"Desat1",
"CG18609",
"CG17562",
"btl",
"trh",
"Gasp",
# "Pcp-1",
"Cpr35B",
"Cpr5C",
"Cpr11A",
"esg",
"Dl",
"bsh",
"eater",
"Hml"
)
```
# miniViolin
```{r miniViolin_set2}
for (gene in gene_list) {
plot <- VlnPlot(EGFP, features = gene, pt.size = 0, combine = FALSE)
p <- plot[[1]] +
theme(legend.position = 'none') +
theme(axis.title.x=element_blank(),
axis.text.x=element_blank(),
axis.ticks.x=element_blank()) +
ylab(gene) +
theme(plot.title = element_blank()) +
theme(axis.text.y = element_text(size = 3)) +
theme(text = element_text(size = 8))
assign(gene, p)
}
# plot <- VlnPlot(EGFP, features = "Pcp-1", pt.size = 0, combine = FALSE)
# Pcp1 <- plot[[1]] +
# theme(legend.position = 'none') +
# theme(axis.title.x=element_blank(),
# axis.text.x=element_blank(),
# axis.ticks.x=element_blank()) +
# ylab("Pcp-1") +
# theme(plot.title = element_blank()) +
# theme(axis.text.y = element_text(size = 3)) +
# theme(text = element_text(size = 8))
x_label <- plot[[1]] +
theme(legend.position = 'none') +
ylab("") +
theme(plot.title = element_blank()) +
theme(axis.text.y = element_text(size = 3)) +
theme(text = element_text(size = 8)) +
theme(axis.text.x = element_text(size = 20))
plot_grid(
Mhc,
Mp20,
Act87E,
Act57B,
Mef2,
Cyp4g1,
Desat1,
CG18609,
CG17562,
btl,
trh,
Gasp,
# Pcp1,
Cpr35B,
Cpr5C,
Cpr11A,
esg,
Dl,
bsh,
eater,
Hml,
x_label, ncol = 1)
```
# Notes
2020-02-05:
* miniViolin plots of known marker genes for all clusters.
Tue Dec 10, 2019:
* Violin plot for EGFP and TSC separately for the last set of genes; Combined violin plot for the same; Combined dot plot for top 5 genes by fold change in all clusters (EGFP: Green and TSC: Red).
Wed Dec 5, 2019:
* Removed three genes: Lsd-1, mdy, Fas1.
Wed Dec 4, 2019:
* Use these selected genes for cluster 0, 1 and 2. Cluster 0: Pli, LpR2, path, apolpp, FASN1, Hnf4, Lsd-1, mdy; Cluster 1: sls, Mlc2, Mlp60A, Mhc, Mf, Mp20; Cluster 2: FASN3, FASN2, LpR1, salm, ImpL2, Fas1.
Sun Dec 1, 2019:
* Dot plot and mini violin plots: 3 top expressed marker genes for dot plot; 2 top for mini-violin plot.
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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