diff options
| -rw-r--r-- | wqflask/wqflask/ctl/ctl_analysis.py | 24 |
1 files changed, 19 insertions, 5 deletions
diff --git a/wqflask/wqflask/ctl/ctl_analysis.py b/wqflask/wqflask/ctl/ctl_analysis.py index 71c41135..44bade5c 100644 --- a/wqflask/wqflask/ctl/ctl_analysis.py +++ b/wqflask/wqflask/ctl/ctl_analysis.py @@ -52,8 +52,10 @@ r_save_image = ro.r["save.image"] # Map the save.image function r_class = ro.r["class"] # Map the class function r_save = ro.r["save"] # Map the save function r_write_table = ro.r["write.table"] # Map the write.table function -r_as_data_frame = ro.r["as.data.frame"] # Map the write.table function -r_data_frame = ro.r["data.frame"] # Map the write.table function +r_read_table = ro.r["read.table"] # Map the read.table function +r_as_data_frame = ro.r["as.data.frame"] # Map the write.table function +r_data_frame = ro.r["data.frame"] # Map the write.table function +r_as_numeric = ro.r["as.numeric"] # Map the write.table function class CTL(object): def __init__(self): @@ -69,6 +71,7 @@ class CTL(object): self.r_lineplot = ro.r["ctl.lineplot"] # Map the ctl.lineplot function self.r_CTLnetwork = ro.r["CTLnetwork"] # Map the CTLnetwork function self.r_CTLprofiles = ro.r["CTLprofiles"] # Map the CTLprofiles function + self.r_CTLsignificant = ro.r["CTLsignificant"] # Map the CTLsignificant function print("Obtained pointers to CTL functions") def run_analysis(self, requestform): @@ -111,21 +114,32 @@ class CTL(object): else: traits.append("-999") - rPheno = r_t(ro.r.matrix(r_unlist(traits), nrow=len(self.trait_db_list), ncol=len(individuals), dimnames = r_list(self.trait_db_list, individuals), byrow=True)) + rPheno = r_t(ro.r.matrix(r_as_numeric(r_unlist(traits)), nrow=len(self.trait_db_list), ncol=len(individuals), dimnames = r_list(self.trait_db_list, individuals), byrow=True)) # Use a data frame to store the objects rPheno = r_data_frame(rPheno) rGeno = r_data_frame(rGeno) + r_write_table(rGeno, "~/outputGN/geno.csv") + r_write_table(rPheno, "~/outputGN/pheno.csv") + # Perform the CTL scan - res = self.r_CTLscan(rGeno, rPheno) + res = self.r_CTLscan(rGeno, rPheno, ncores = 6) + + # Get significant interactions + significant = self.r_CTLsignificant(res) + + print(significant[0]) # Create an image for output self.results = {} self.results['imgurl'] = webqtlUtil.genRandStr("WGCNAoutput_") + ".png" self.results['imgloc'] = GENERATED_IMAGE_DIR + self.results['imgurl'] + self.results['ctlresult'] = significant + + # Create the lineplot r_png(self.results['imgloc'], width=1000, height=600) - self.r_lineplot(res, significance = 1) + self.r_lineplot(res) r_dev_off() # Flush any output from R |