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Beatrice Tan
CNAprioritization
Commits
80a92bce
Commit
80a92bce
authored
Feb 07, 2018
by
Beatrice Tan
Browse files
Fixed merge conflicts.
parents
4a39be4b
42ec6850
Changes
5
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config.yaml
View file @
80a92bce
#Directories to be specified
#
workdir: /home/bftan/CNA_results #directory to write output
#
gisticdir: /home/bftan/Tools/GISTIC2 #directory to install GISTIC2
workdir
:
/home/bftan/CNA_results
#directory to write output
gisticdir
:
/home/bftan/Tools/GISTIC2
#directory to install GISTIC2
#workdir: /home/bftan/CNA_results #directory to write output
#gisticdir: /home/bftan/Tools/GISTIC2 #directory to install GISTIC2
workdir
:
/home/beatrice/CNA_analysis
gisticdir
:
/home/beatrice/CNA_analysis/run_gistic2
#workdir: /home/beatrice/CNA_analysis
#gisticdir: /home/beatrice/CNA_analysis/run_gistic2
#Input details to download from firehose
cancer_type
:
SKCM
...
...
rules/ComparisonSettings.smk
View file @
80a92bce
...
...
@@ -10,8 +10,8 @@ rule gistic_settings:
seg="Input/Segments_tumor.txt",
lambda wildcards: config["comparison_settings"][wildcards.setting]
output:
"Settings/GISTIC_
wildcards.
setting/all_lesions.conf_" + config["gistic_precision"] + ".txt",
"Settings/GISTIC_
wildcards.
setting/regions_track.conf_" + config["gistic_precision"] + ".bed"
expand(
"Settings/GISTIC_
{
setting
_nr}
/all_lesions.conf_" + config["gistic_precision"] + ".txt",
setting_nr=range(len(config["comparison_settings"]))),
"Settings/GISTIC_
{
setting
_nr}
/regions_track.conf_" + config["gistic_precision"] + ".bed"
params:
cnv="",
ref=config["reference"],
...
...
rules/GenePrioritization.smk
View file @
80a92bce
...
...
@@ -3,7 +3,8 @@ rule do_GO_analysis:
input:
gene_list="Reports/Genes_{tool}.txt"
output:
go="GO/{tool}.txt"
table="GO/Enriched_GOs_{tool}.txt",
plot="GO/Enriched_GOs_{tool}.jpg"
params:
organism="hsapiens", #default is human
ontology="BP", #MF, BP, CC or all
...
...
@@ -16,7 +17,7 @@ rule do_GO_analysis:
rule compare_enriched_GOs:
"""Compare the top 50 GO terms detected by RUBIC and GISTIC2.0"""
input:
go=expand("GO/{tool}.txt", tool=["GISTIC2", "RUBIC"])
go=expand("GO/
Enriched_GOs_
{tool}.txt", tool=["GISTIC2", "RUBIC"])
output:
"GO/comparison.txt"
run:
...
...
scripts/ReportTools.py
View file @
80a92bce
...
...
@@ -106,12 +106,13 @@ def venn3_overlap(gene_lists, known_genes, out_venn):
def
plot_histogram_sizes
(
parsed_results
,
plot_file
):
"""Make boxplot with swarmplot on top showing sizes of recurrent regions detected by GISTIC2.0 and RUBIC."""
size_list
,
size_list_known
=
parse_sizes_for_plot
(
parsed_results
)
print
(
size_list_known
)
sns
.
set_style
(
"white"
)
f
,
ax
=
plt
.
subplots
(
figsize
=
(
7
,
7
))
ax
.
set
(
yscale
=
"log"
)
g
=
sns
.
boxplot
(
x
=
"Tool"
,
y
=
"Size"
,
hue
=
"CNV type"
,
data
=
size_list
,
whis
=
np
.
inf
,
palette
=
{
"Amplification"
:
"#71AEC0"
,
"Deletion"
:
"#B55D60"
})
g
=
sns
.
swarmplot
(
x
=
"Tool"
,
y
=
"Size"
,
dodge
=
True
,
hue
=
"CNV type"
,
data
=
size_list
,
size
=
5
,
palette
=
{
"Amplification"
:
"#527F8C"
,
"Deletion"
:
"#844446"
})
g
=
sns
.
swarmplot
(
x
=
"Tool"
,
y
=
"Size"
,
dodge
=
True
,
hue
=
"CNV type"
,
data
=
size_list_known
,
size
=
5
,
palette
=
{
"Amplification"
:
"black"
,
"Deletion"
:
"black"
})
#
g = sns.swarmplot(x="Tool", y="Size", dodge=True, hue="CNV type", data=size_list_known, size=5, palette={"Amplification": "black", "Deletion": "black"})
sns
.
despine
()
g
.
set_xlabel
(
"Tool"
,
fontsize
=
16
)
g
.
set_ylabel
(
"Log size of recurrent regions"
,
fontsize
=
16
)
...
...
wrappers/topgo/wrapper.R
View file @
80a92bce
...
...
@@ -48,5 +48,7 @@ print(allRes)
write.table
(
allRes
,
file
=
snakemake
@
output
[[
1
]],
quote
=
FALSE
,
sep
=
"\t"
,
eol
=
"\n"
)
#Visualize GO term relationships
jpeg
(
snakemake
@
output
[[
1
]])
showSigOfNodes
(
GOdata
,
score
(
resultFisher
),
firstSigNodes
=
5
,
useInfo
=
'all'
)
printGraph
(
GOdata
,
resultFisher
,
firstSigNodes
=
5
,
fn.prefix
=
"tGO"
,
useInfo
=
"all"
,
pdfSW
=
TRUE
)
dev.off
()
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