biopipen 0.31.2__py3-none-any.whl → 0.31.4__py3-none-any.whl

biopipen/__init__.py

@@ -1 +1 @@
-__version__ = "0.31.2"
+__version__ = "0.31.4"

biopipen/ns/plot.py

@@ -35,7 +35,7 @@ class VennDiagram(Proc):
     envs = {
         "inopts": {"row.names": -1, "header": False},
         "intype": "raw",
-        "devpars": {"res": 100, "width": 1000, "height": 1000},
+        "devpars": {"res": 100, "width": 800, "height": 600},
         "args": {},
         "ggs": None,
     }

biopipen/scripts/plot/VennDiagram.R

@@ -1,8 +1,6 @@
 {{ biopipen_dir | joinpaths: "utils", "io.R" | source_r }}
 {{ biopipen_dir | joinpaths: "utils", "plot.R" | source_r }}
 
-library(dplyr)
-
 infile = {{in.infile | quote}}
 outfile = {{out.outfile | quote}}
 inopts = {{envs.inopts | r}}
@@ -18,9 +16,7 @@ if (intype == "raw") {
     indata = lapply(indata, function(x) unlist(strsplit(x, ",", fixed=TRUE)))
 } else { # computed
     elems = rownames(indata)
-    indata = indata %>%
-        mutate(across(everything(), function(x) elems[as.logical(x)])) %>%
-        as.list()
+    indata = apply(indata, 2, function(x) elems[as.logical(x)])
 }
 
 plotVenn(

biopipen/scripts/scrna/SeuratMap2Ref.R

@@ -90,8 +90,8 @@ for (rname in names(mapquery_args$refdata)) {
     }
 }
 
-if (refnorm == "auto" && .is_sct(reference)) {
-    refnorm = "SCTransform"
+if (refnorm == "auto") {
+    refnorm = ifelse (.is_sct(reference), "SCTransform", "NormalizeData")
 }
 if (refnorm == "SCTransform") {
     # Check if the reference is SCTransform'ed
@@ -110,7 +110,7 @@ if (refnorm == "SCTransform") {
 } else if (refnorm == "NormalizeData") {
     findtransferanchors_args$normalization.method = "LogNormalize"
 } else {
-    stop("Unknown normalization method: {refnorm}")
+    stop(paste0("Unknown normalization method: ", refnorm))
 }
 
 # Load Seurat object

biopipen/scripts/tcr/CDR3AAPhyschem.R

@@ -169,9 +169,12 @@ immdata = readRDS(immdatafile)
 
 merge_data = function(sam) {
     # Merge the data for one sample from immdata and metadata
-    out = immdata$data[[sam]] %>%
-        separate_rows(chain, CDR3.aa, V.name, J.name, sep = ";") %>%
-        filter(chain == "TRB") %>%
+    out = immdata$data[[sam]]
+    if ("chain" %in% colnames(out)) {
+        out = out %>% separate_rows(chain, CDR3.aa, V.name, J.name, sep = ";") %>%
+            filter(chain == "TRB")
+    }
+    out = out %>%
         mutate(
             Sample = sam,
             locus = "TCRB",

biopipen/scripts/tcr/TCRClustering.R

@@ -35,12 +35,11 @@ if (is.null(prefix)) { prefix = "" }
 
 get_cdr3aa_df = function() {
     out = expand_immdata(immdata, cell_id = "Barcode") %>%
-        mutate(Barcode = glue(paste0(prefix, "{Barcode}"))) %>%
-        select(Barcode, CDR3.aa, chain)
+        mutate(Barcode = glue(paste0(prefix, "{Barcode}")))
 
     if (on_multi) {
         out$CDR3.aa = sub(";", "", out$CDR3.aa)
-    } else {
+    } else if ("chain" %in% colnames(out)) {
         out = out %>% separate_rows(chain, CDR3.aa, sep = ";") %>%
             filter(chain == "TRB")
     }
@@ -170,7 +169,7 @@ prepare_input = function() {
         sdata = seqdata[[sample]]
         if (on_multi) {
             sdata[[cdr3col]] = sub(";", "", sdata[[cdr3col]])
-        } else {
+        } else if ("chain" %in% colnames(sdata)) {
             sdata = sdata %>% separate_rows(chain, cdr3col, sep = ";") %>%
                 filter(chain == "TRB")
         }

biopipen/utils/plot.R

@@ -10,7 +10,7 @@ plotVenn = function(
     # Extra ggplot components in string
     ggs = NULL,
     # Parameters for device (res, width, height) for `png()`
-    devpars = list(res=100, width=1000, height=1000),
+    devpars = list(res=100, width=800, height=600),
     # The output file. If NULL, will return the plot object
     outfile = NULL
 ) {

{biopipen-0.31.2.dist-info → biopipen-0.31.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: biopipen
-Version: 0.31.2
+Version: 0.31.4
 Summary: Bioinformatics processes/pipelines that can be run from `pipen run`
 License: MIT
 Author: pwwang
@@ -18,5 +18,5 @@ Requires-Dist: pipen-board[report] (>=0.16,<0.17)
 Requires-Dist: pipen-cli-run (>=0.14,<0.15)
 Requires-Dist: pipen-filters (>=0.14,<0.15)
 Requires-Dist: pipen-poplog (>=0.2.0,<0.3.0)
-Requires-Dist: pipen-runinfo (>=0.7,<0.8) ; extra == "runinfo"
+Requires-Dist: pipen-runinfo (>=0.8,<0.9) ; extra == "runinfo"
 Requires-Dist: pipen-verbose (>=0.12,<0.13)

{biopipen-0.31.2.dist-info → biopipen-0.31.4.dist-info}/RECORD

@@ -1,4 +1,4 @@
-biopipen/__init__.py,sha256=Me03yXizCG2hXimVttvq6I-XoZSxSRE2J-NrK4My4cU,23
+biopipen/__init__.py,sha256=ZRJesu3_rpj9DcGHrsN5Zl7GDxuBTLAkcDxRMvMJE5c,23
 biopipen/core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biopipen/core/config.py,sha256=edK5xnDhM8j27srDzsxubi934NMrglLoKrdcC8qsEPk,1069
 biopipen/core/config.toml,sha256=7IXvviRicZ2D1h6x3BVgbLJ96nsh-ikvZ0sVlQepqFE,1944
@@ -18,7 +18,7 @@ biopipen/ns/delim.py,sha256=fejsh4KW1TG5oMZzAC238LvQhBz7brXkfl3BHfnLK5M,5612
 biopipen/ns/gene.py,sha256=rty-Bjcf87v2vyb9X4kRvfrQ6XQYXgN4f2ftFO0nWA8,3888
 biopipen/ns/gsea.py,sha256=EsNRAPYsagaV2KYgr4Jv0KCnZGqayM209v4yOGGTIOI,7423
 biopipen/ns/misc.py,sha256=qXcm0RdR6W-xpYGgQn3v7JBeYRWwVm5gtgSj2tdVxx4,2935
-biopipen/ns/plot.py,sha256=_dGLKpyHiJqLIIQu5tqCk8H5BkgGBh_qRUZHkjnOgtE,18080
+biopipen/ns/plot.py,sha256=XzLq0A8qCIQRbxhPEdWhEfbRZ8g3e4KriVz0RP8enNY,18078
 biopipen/ns/regulatory.py,sha256=qvc9QrwgwCI_lg0DQ2QOZbAhC8BAD1qnQXSGtAGlVcY,11750
 biopipen/ns/rnaseq.py,sha256=bKAa6friFWof4yDTWZQahm1MS-lrdetO1GqDKdfxXYc,7708
 biopipen/ns/scrna.py,sha256=fXP_h7gchcuk_Jwos0IgY_P8ON6Q995OgKHgdrxfvAY,112868
@@ -120,7 +120,7 @@ biopipen/scripts/plot/Manhattan.R,sha256=7lJwCX1d0zUpJVhVcmQ35ZtQELzkaDNnBTNHHc3
 biopipen/scripts/plot/QQPlot.R,sha256=Xil19FJ7jbsxo1yU7dBhhZo2_95Gz6gpTyuv9F0RDNM,4115
 biopipen/scripts/plot/ROC.R,sha256=cjmmYRQycYisqRmlkZE9nbmwfo-04wdJKVmlOsiEFAM,2451
 biopipen/scripts/plot/Scatter.R,sha256=fg4H5rgdr6IePTMAIysiElnZme0vCh1T0wrwH2Q9xkM,2840
-biopipen/scripts/plot/VennDiagram.R,sha256=IQG4OLXdORbmKMWca7dtSDX_RdH8FCrpDfi3eMae7G8,773
+biopipen/scripts/plot/VennDiagram.R,sha256=Am9umSGr2QxZc2MIMGMBhpoEqta3qt_ItF-9_Y53SXE,704
 biopipen/scripts/regulatory/MotifAffinityTest.R,sha256=1sR3sWRZbxDeFO290LcpzZglzOLc13SSvibDON96PCg,8852
 biopipen/scripts/regulatory/MotifAffinityTest_AtSNP.R,sha256=SAyTm2-6g5qVJFRrLxEY0QJrLWTkwDi_J_9J7HhtTN8,4438
 biopipen/scripts/regulatory/MotifAffinityTest_MotifBreakR.R,sha256=wCK4tLx1iWh_OwW7ZvLTCjTGWCIfVqw-lYC0-JqIPqg,3338
@@ -164,7 +164,7 @@ biopipen/scripts/scrna/SeuratClustering-common.R,sha256=JX4Cn2FC6GOcBqaVyGDD3MM5
 biopipen/scripts/scrna/SeuratClustering.R,sha256=0OKRBQ5rFuupK7c03_sSt2HMwMdMnCYFqTvkRXFKchs,1706
 biopipen/scripts/scrna/SeuratFilter.R,sha256=BrYK0MLdaTtQvInMaQsmOt7oH_hlks0M1zykkJtg2lM,509
 biopipen/scripts/scrna/SeuratLoading.R,sha256=ekWKnHIqtQb3kHVQiVymAHXXqiUxs6KKefjZKjaykmk,900
-biopipen/scripts/scrna/SeuratMap2Ref.R,sha256=KARt5IVBDYpNhLZ7_j0FEi1u5S8PxU_mB4THH26s7AM,12008
+biopipen/scripts/scrna/SeuratMap2Ref.R,sha256=B0RZ2k1IUKdhe34SjU-8CxvYGj7ub-z7JJaSE0snCok,12040
 biopipen/scripts/scrna/SeuratMetadataMutater.R,sha256=PMwG0Xvl_EEVKkicfrIi4arEqpY948PkYLkb59kTAXI,1135
 biopipen/scripts/scrna/SeuratPreparing-common.R,sha256=WuD7lGS17eAUQWSiIdAoV0EIeqS3Tnkkx-7PbP6Q3tc,16279
 biopipen/scripts/scrna/SeuratPreparing-doublet_detection.R,sha256=TNN2lfFjpnnO0rguMsG38JYCP1nFUhcPLJ1LqGj-Sc8,6674
@@ -202,7 +202,7 @@ biopipen/scripts/tcgamaf/Maf2Vcf.py,sha256=Cxh7fiSNCxWDTfIJqZDOOnaSrw-85S_fH2U-P
 biopipen/scripts/tcgamaf/MafAddChr.py,sha256=V10HMisl12O3ZfXuRmFNdy5p-3mr43WCvy0GHxSpwfA,494
 biopipen/scripts/tcgamaf/maf2vcf.pl,sha256=hJKcH-NbgWK6fmK7f3qex7ozJJl-PqCNPXqpwfcHwJg,22707
 biopipen/scripts/tcr/Attach2Seurat.R,sha256=0KZaBkuPvqOBXq4ZG3pzIIua5HL-161K5dVXRoCysy4,1366
-biopipen/scripts/tcr/CDR3AAPhyschem.R,sha256=_eg5Ep-Zt-J-VklYrklDPYAvZTBH_RIxbLTPJDqS4KE,16753
+biopipen/scripts/tcr/CDR3AAPhyschem.R,sha256=ZxHyn4vJF-1PDbnbozovOipET_QZKqeFrKUibRpLgzw,16825
 biopipen/scripts/tcr/CloneResidency.R,sha256=KAcFB39vTYsk8IEj44s8oSFVhKjpAdJ8hkpKxtdWzRA,21540
 biopipen/scripts/tcr/CloneSizeQQPlot.R,sha256=hds1C80Q_W40Ikp-BrFfvh_aBf_V61lz-1YAvkDESyk,4569
 biopipen/scripts/tcr/GIANA/GIANA.py,sha256=0qLhgCWxT8K-4JvORA03CzBPTT5pd4Di5B_DgrHXbFA,47198
@@ -225,7 +225,7 @@ biopipen/scripts/tcr/ImmunarchLoading.R,sha256=Vw2oIza3mDJzg9kuo-w5jvwdivk4AtDA6
 biopipen/scripts/tcr/ImmunarchSplitIdents.R,sha256=FGCeGV0uSmFU91lKkldUAeV4A2m3hHw5X4GNi8ffGzI,1873
 biopipen/scripts/tcr/SampleDiversity.R,sha256=oipN4-2nQZe8bYjI0lZ0SvZ7T8GZ_FWkpkobi1cwmWE,2664
 biopipen/scripts/tcr/TCRClusterStats.R,sha256=QhXgfKSh27VHO901hDizyGYTXMYFJxW22StchQUq3uE,12906
-biopipen/scripts/tcr/TCRClustering.R,sha256=J3cBAK3PRN54iQHMISVSbldhVDWPIWfeO8Vrjr9qwyE,9571
+biopipen/scripts/tcr/TCRClustering.R,sha256=MRCaFbgMhhW9uimVBrE1Q5VqqxQpnKv5W2ILWmHdkU8,9593
 biopipen/scripts/tcr/TCRDock.py,sha256=jjzxMWp-hs0LDtA1mVbiWDvUieSO7X-F9yeKGy1LSTM,3026
 biopipen/scripts/tcr/TESSA.R,sha256=XFC2P_e_Gm83jG5EjzVIW6KcyG5IieAaK7sXDA3_oZ0,6864
 biopipen/scripts/tcr/TESSA_source/Atchley_factors.csv,sha256=SumqDOqP67P54uM7Cuc5_O_rySTWcGo7eX3psMSPX9s,763
@@ -274,12 +274,12 @@ biopipen/utils/io.R,sha256=jIYdqdn0iRWfQYAZa5CjXi3fikqmYvPPLIXhobRe8sw,537
 biopipen/utils/misc.R,sha256=qTninxi9XAM_3QJqwThflGA-j7p1aKpQ9Pjmix6Iy3U,12059
 biopipen/utils/misc.py,sha256=nkQHa3GMc7Ce0N2GKmucbRc8BMXgZ2yr_SPbq9RYA4s,3740
 biopipen/utils/mutate_helpers.R,sha256=Bqy6Oi4rrPEPJw0Jq32bVAwwBfZv7JJL9jFcK5x-cek,17649
-biopipen/utils/plot.R,sha256=pzl37PomNeUZPxohHZ2w93j3Fc4T0Qrc62FF-9MTKdw,4417
+biopipen/utils/plot.R,sha256=fmWnCv6EpOU8NvHFvShbdPRqB659vHcDlJAqWIXM8XQ,4415
 biopipen/utils/reference.py,sha256=oi5evicLwHxF0KAIPNZohBeHJLJQNWFJH0cr2y5pgcg,5873
 biopipen/utils/rnaseq.R,sha256=Ro2B2dG-Z2oVaT5tkwp9RHBz4dp_RF-JcizlM5GYXFs,1298
 biopipen/utils/single_cell.R,sha256=pJjYP8bIZpNAtTQ32rOXhZxaM1Y-6D-xUcK3pql9tbk,4316
 biopipen/utils/vcf.py,sha256=ajXs0M_QghEctlvUlSRjWQIABVF02wPdYd-0LP4mIsU,9377
-biopipen-0.31.2.dist-info/METADATA,sha256=3C7vpZEWG0ySF1H298xWctBRl77fl7NZluVa7Q65jUc,882
-biopipen-0.31.2.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-biopipen-0.31.2.dist-info/entry_points.txt,sha256=69SbeMaF47Z2DS40yo-qDyoBKmMmumrNnsjEZMOioCE,625
-biopipen-0.31.2.dist-info/RECORD,,
+biopipen-0.31.4.dist-info/METADATA,sha256=-ZA3ibCLubauXddI46VdKgbKvzBKiLR8sk0HWQArEZo,882
+biopipen-0.31.4.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+biopipen-0.31.4.dist-info/entry_points.txt,sha256=69SbeMaF47Z2DS40yo-qDyoBKmMmumrNnsjEZMOioCE,625
+biopipen-0.31.4.dist-info/RECORD,,