From 4bec8bee7e630ed2b6908989c422dced53ccd902 Mon Sep 17 00:00:00 2001
From: dimit98 <dimit98@mi.fu-berlin.de>
Date: Sat, 24 Oct 2020 15:45:58 +0200
Subject: [PATCH] minor changes
---
rules/clustering.smk | 5 ++---
scripts/differential_testing.R | 8 --------
scripts/enrichment_vis.R | 2 --
scripts/gene_set_analysis.py | 18 ------------------
4 files changed, 2 insertions(+), 31 deletions(-)
diff --git a/rules/clustering.smk b/rules/clustering.smk
index 469c0c8..bb36875 100644
--- a/rules/clustering.smk
+++ b/rules/clustering.smk
@@ -19,7 +19,6 @@ rule clustering_louvain:
genes = config["clustering"]["genes_to_vis"],
subclustering = config["clustering"]["subclustering"],
clustering_resolution = config["clustering"]["clustering_resolution"],
- #subclustering_resolution = config["clustering"]["subclustering_resolution"]
script:
"../scripts/clustering.py"
@@ -41,7 +40,8 @@ rule specter:
rule clustering_specter:
input:
- expand("file_dir/post_vis_data_{downsampling}.h5ad", downsampling=config["downsampling"]["downsampling_method"])
+ expand("file_dir/post_vis_data_{downsampling}.h5ad", downsampling=config["downsampling"]["downsampling_method"]),
+ "file_dir/specter_clustering.csv"
output:
"file_dir/post_clustering_specter.h5ad",
"file_dir/annotation_list_specter.npy",
@@ -60,7 +60,6 @@ rule clustering_specter:
genes = config["clustering"]["genes_to_vis"],
subclustering = config["clustering"]["subclustering"],
clustering_resolution = config["clustering"]["clustering_resolution"],
- #subclustering_resolution = config["clustering"]["subclustering_resolution"]
script:
"../scripts/clustering_specter.py"
diff --git a/scripts/differential_testing.R b/scripts/differential_testing.R
index 593bdb8..b047fa3 100644
--- a/scripts/differential_testing.R
+++ b/scripts/differential_testing.R
@@ -63,17 +63,9 @@ result_ent[,FDR:=p.adjust(`Pr(>Chisq)`, 'fdr')]
ent_de = result_ent[result_ent$FDR<as.numeric(snakemake@config[["differential_testing"]][["DE_threshold"]]),, drop=F]
ent_de = ent_de[order(ent_de$FDR),]
-print("hier kommt DE_threshold")
-print(as.numeric(snakemake@config[["differential_testing"]][["DE_threshold"]]))
-#ent_all = result_ent[order(result_ent$FDR),]
-
name_of_csv = paste("results/",name,"_diff_testing.csv", sep="")
write.csv(ent_de, name_of_csv, row.names=FALSE)
-#name_of_csv2 = paste("results/",name,"_diff_testing.csv", sep="")
-#write.csv(ent_all,name_of_csv2, row.names=FALSE)
-
-print("done mit einem Durchlauf")
}
diff --git a/scripts/enrichment_vis.R b/scripts/enrichment_vis.R
index 87d87b3..a643f2b 100644
--- a/scripts/enrichment_vis.R
+++ b/scripts/enrichment_vis.R
@@ -1,8 +1,6 @@
library("dplyr")
library("ggplot2")
-print(snakemake@wildcards[["cluster"]])
-
name <- snakemake@wildcards[["cluster"]]
data <- read.csv(file = snakemake@input[[1]])
diff --git a/scripts/gene_set_analysis.py b/scripts/gene_set_analysis.py
index 82d5f2b..e1236c9 100644
--- a/scripts/gene_set_analysis.py
+++ b/scripts/gene_set_analysis.py
@@ -1,11 +1,6 @@
import pandas as pd
from gprofiler import GProfiler
import gprofiler
-#import matplotlib.pyplot as plt
-#import os
-print("EN_threshold")
-print(float(snakemake.params.EN_threshold))
-print(snakemake.wildcards.cluster)
file = pd.read_csv("results/"+ snakemake.wildcards.cluster +"_diff_testing.csv")
@@ -19,16 +14,3 @@ enrich_results = enrichment.set_index('native').sort_values('p_value').iloc[:,[2
enrich_results.to_csv("results/"+snakemake.wildcards.cluster+"_enrich_results.csv", sep=",")
-#from gprofiler_plotting import plot_enrich
-
-
-#plt.figure(1)
-#heatmap = sb.heatmap(cell_annotation_norm, cbar=False, annot=True)
-#heatmap.autoscale()
-#heatmap = heatmap.get_figure()
-#heatmap.savefig("figures/marker_genes_32_4.png")
-
-#plt.figure(1)
-#temp = plot_enrich(paneth_enrich_results)
-#temp = temp.get_figure()
-#temp.savefig("figures/paneth_enrich_graph.jpg")
--
GitLab