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Commit 89c8073f authored by Dimitrios Kyriakis's avatar Dimitrios Kyriakis
Browse files

coll

parent 2c3694af
......@@ -36,7 +36,8 @@ EBs are cells at an early stage of spontaneous differentiation. Scorecard analys
## Libraries
<details><summary>Code</summary>
<p>
```{r libraries}
```r
library(reticulate)
use_python("C:/Users/dimitrios.kyriakis/AppData/Local/Continuum/anaconda3/envs/iscwrapper/python.exe", required = TRUE)
options(future.globals.maxSize= 2122317824)
......@@ -63,7 +64,8 @@ set.seed(123)
## Setting Up
<details><summary>Code</summary>
<p>
```{r setup}
```r
tool="seurat"
project ="Michi_Data"
dataset <- project
......@@ -103,7 +105,8 @@ Additional to this filtering, we defined cells as low-quality, based on three cr
<details><summary>Code</summary>
<p>
```{r readfiles}
```r
NewDir <- paste0(Sys.Date(),"_",tool,"_elbow_",elbow,"_Mito-",remove_mt,"_Ribo-",remove_ribsomal,"_SCT-",SCT,"_criteria_pass-",criteria_pass)
dir.create(NewDir)
setwd(NewDir)
......@@ -119,6 +122,7 @@ Combined <- Return_fun$Combined
Data_List <- Return_fun$Data_List
setwd("../")
```
</p>
</details>
......@@ -135,7 +139,8 @@ The integration of the filtered matrices of the different datasets was performed
<details><summary>Code</summary>
<p>
```{r remapping}
```r
dir.create("Aligned_Cond_RegPhase")
setwd("Aligned_Cond_RegPhase")
DefaultAssay(Combined) <- "RNA"
......@@ -159,6 +164,7 @@ DefaultAssay(object = Seurat.combined) <- "integrated"
Combined <- Seurat.combined
setwd("../")
```
</p>
</details>
......@@ -172,7 +178,8 @@ The clustering of data was performed using Louvain clustering. The resolution of
<details><summary>Code</summary>
<p>
```{r Clustering}
```r
dir.create("Clusters")
setwd("Clusters")
Combined <- ICSWrapper::reduce_dim(Combined,project=project,assay = "SCT")$Combined#,resolution=c(0.1))$Combined
......@@ -228,7 +235,8 @@ A short list of manually curated markers was used in order to validate the diffe
<details><summary>Code</summary>
<p>
```{r Developmental_Markers}
```r
# ================================== Developmental Stages =========================================
dir.create("Developmental_Markers")
setwd("Developmental_Markers")
......@@ -274,7 +282,8 @@ setwd("../")
<details><summary>Code</summary>
<p>
```{r Pairwise DF}
```r
# =============================== PAIRWISE DF ===============================================
dir.create("DF_Pairwise_PAPER")
setwd("DF_Pairwise_PAPER")
......@@ -335,6 +344,7 @@ pairwise_df <- function (comb,object,cl_combinations){
}
# Apply DF
mclapply(c(1:dim(cl_combinations)[2]),FUN=pairwise_df,object=Combined,cl_combinations=cl_combinations,mc.cores=1)
```
</p>
</details>
......@@ -344,7 +354,8 @@ mclapply(c(1:dim(cl_combinations)[2]),FUN=pairwise_df,object=Combined,cl_combina
<details><summary>Code</summary>
<p>
```{r gene intersection}
```r
dirs_pairs <- list.dirs("C:/Users/dimitrios.kyriakis/Desktop/PhD/Projects/Michi_Data/DF_Pairwise_Networks/DF_Pairwise_PAPER",full.names = TRUE )[-1]
dirs_pairs <- grep('IPSC|D06.*D06|D15.*D15|D21.*D21',dirs_pairs,value = TRUE)
dirs_pairs <- dirs_pairs[-4]
......
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