Skip to content

Volcano EC gosplit fix #32

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
jraysajulga wants to merge 7 commits into
base: master
Choose a base branch
from
Open

Volcano EC gosplit fix #32

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
7 commits
Select commit Hold shift + click to select a range
35a30d3
condense ifelse conditional for is_in_db function
jraysajulga Mar 29, 2019
8d9a8b8
fix incorrect filename for tax_check
jraysajulga Mar 29, 2019
996cca9
simplify slim-ancestors loop
jraysajulga Mar 29, 2019
e0b1171
Merge branch 'master' of https://github.com/jraysajulga/metaquantome
jraysajulga May 20, 2019
81e3f20
add ontology check to volcano viz to ensure gosplit param is not fals…
jraysajulga May 20, 2019
60c702d
remove vestigial testing variable
jraysajulga May 20, 2019
941406b
delete
jraysajulga May 20, 2019
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions metaquantome/cli.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -43,6 +43,7 @@ def cli():
img=args.img,
infile=args.infile,
mode=args.mode,
ontology=args.ontology,
meancol=args.meancol,
nterms=args.nterms,
strip=args.strip,
Expand Down
4 changes: 2 additions & 2 deletions metaquantome/modules/run_viz.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@

def run_viz(plottype, img, infile, strip=None,
mode=None, meancol=None, nterms='5', target_rank=None, barcol=6, # barplot
textannot=None, fc_name=None, flip_fc=False, gosplit=False, # volcano
textannot=None, fc_name=None, flip_fc=False, gosplit=False, ontology=None, # volcano
sinfo=None, filter_to_sig=False, alpha='0.05', # heatmap
calculate_sep=False, # pca
whichway=None, name=None, id=None, target_onto=None, # ft_dist
Expand All @@ -24,7 +24,7 @@ def run_viz(plottype, img, infile, strip=None,
if plottype == "bar":
cmd += [mode, meancol, nterms, width, height, target_rank, target_onto, barcol, tabfile]
elif plottype == "volcano":
cmd += [str(textannot), fc_name, flip_fc, gosplit, width, height, tabfile]
cmd += [str(textannot), fc_name, flip_fc, ontology, gosplit, width, height, tabfile]
elif plottype == "heatmap":
samp_grps = SampleGroups(sinfo)
all_intcols_str = ','.join(samp_grps.all_intcols)
Expand Down
16 changes: 9 additions & 7 deletions metaquantome/modules/viz.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -479,19 +479,21 @@ volcano_cli <- function(args){
# 4. name of text annotation column
# 5. name of fold change column
# 6. whether to flip fc
# 7. whether to split GO by ontology/namespace
# 8. image width (default 5)
# 9. image height (default 5)
# 7. ontology
# 8. whether to split GO by ontology/namespace
# 9. image width (default 5)
# 10. image height (default 5)
img <- args[2]
infile <- args[3]
df <- read_result(infile)
textannot <- args[4]
fc_name <- args[5]
flip_fc <- (args[6] == "True")
gosplit <- (args[7] == "True")
width <- as.numeric(args[8])
height <- as.numeric(args[9])
tabfile <- args[10]
ontology <- args[7]
gosplit <- (args[8] == "True" & ontology == "go")
width <- as.numeric(args[9])
height <- as.numeric(args[10])
tabfile <- args[11]
if (tabfile == "None") tabfile <- NULL
plt <- mq_volcano(df, img=img, textannot=textannot, fc_name=fc_name,
flip_fc=flip_fc, gosplit=gosplit, width=width, height=height,
Expand Down