Merge pull request #815 from UTSouthwesternDSSR/main

Attempt to identify tumor cells in those non-ETP samples without B cells (SCPCP000003)

.github/workflows/run_cell-type-nonETP-ALL-03.yml

@@ -89,4 +89,5 @@ jobs:
           # run module script(s) here
           Rscript scripts/00-01_processing_rds.R
           Rscript scripts/02-03_annotation.R
-          Rscript scripts/multipanel_plot.R
+          Rscript scripts/04_multipanel_plot.R
+          Rscript scripts/05_cluster_evaluation.R

analyses/cell-type-nonETP-ALL-03/renv.lock

@@ -76,6 +76,41 @@
       ],
       "Hash": "3aec5928ca10897d7a0a1205aae64627"
     },
+    "BiocNeighbors": {
+      "Package": "BiocNeighbors",
+      "Version": "1.22.0",
+      "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
+      "Requirements": [
+        "BiocParallel",
+        "Matrix",
+        "Rcpp",
+        "RcppHNSW",
+        "S4Vectors",
+        "methods",
+        "stats"
+      ],
+      "Hash": "da9f332c88453734623406dcca13ee03"
+    },
+    "BiocParallel": {
+      "Package": "BiocParallel",
+      "Version": "1.38.0",
+      "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
+      "Requirements": [
+        "BH",
+        "R",
+        "codetools",
+        "cpp11",
+        "futile.logger",
+        "methods",
+        "parallel",
+        "snow",
+        "stats",
+        "utils"
+      ],
+      "Hash": "7b6e79f86e3d1c23f62c5e2052e848d4"
+    },
     "BiocVersion": {
       "Package": "BiocVersion",
       "Version": "3.19.1",
@@ -433,6 +468,13 @@
       ],
       "Hash": "c92ba8b9a2c5c9ff600a1062a3b7b727"
     },
+    "RhpcBLASctl": {
+      "Package": "RhpcBLASctl",
+      "Version": "0.23-42",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "c966ea2957ff75e77afa5c908dfc89e1"
+    },
     "Rtsne": {
       "Package": "Rtsne",
       "Version": "0.17",
@@ -717,6 +759,25 @@
       "Repository": "CRAN",
       "Hash": "da69e6b6f8feebec0827205aad3fdbd8"
     },
+    "bluster": {
+      "Package": "bluster",
+      "Version": "1.14.0",
+      "Source": "Bioconductor",
+      "Repository": "Bioconductor 3.19",
+      "Requirements": [
+        "BiocNeighbors",
+        "BiocParallel",
+        "Matrix",
+        "Rcpp",
+        "S4Vectors",
+        "cluster",
+        "igraph",
+        "methods",
+        "stats",
+        "utils"
+      ],
+      "Hash": "ed9597168d850071aa9abbbef7be7204"
+    },
     "bslib": {
       "Package": "bslib",
       "Version": "0.8.0",
@@ -840,6 +901,7 @@
       "RemoteSha": "d7d6569ae9e30bf774908301af312f626de4cbd5",
       "Requirements": [
         "MCMCpack",
+        "R",
         "RColorBrewer",
         "cluster",
         "dlm",
@@ -848,7 +910,7 @@
         "parallel",
         "parallelDist"
       ],
-      "Hash": "efd05c69dffe1128eb4843f3107eb606"
+      "Hash": "e356046a6ab19635791f7ce46ecd5991"
     },
     "cowplot": {
       "Package": "cowplot",
@@ -1083,6 +1145,32 @@
       ],
       "Hash": "c2efdd5f0bcd1ea861c2d4e2a883a67d"
     },
+    "forcats": {
+      "Package": "forcats",
+      "Version": "1.0.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "cli",
+        "glue",
+        "lifecycle",
+        "magrittr",
+        "rlang",
+        "tibble"
+      ],
+      "Hash": "1a0a9a3d5083d0d573c4214576f1e690"
+    },
+    "formatR": {
+      "Package": "formatR",
+      "Version": "1.14",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "63cb26d12517c7863f5abb006c5e0f25"
+    },
     "fs": {
       "Package": "fs",
       "Version": "1.6.4",
@@ -1094,6 +1182,29 @@
       ],
       "Hash": "15aeb8c27f5ea5161f9f6a641fafd93a"
     },
+    "futile.logger": {
+      "Package": "futile.logger",
+      "Version": "1.4.3",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "futile.options",
+        "lambda.r",
+        "utils"
+      ],
+      "Hash": "99f0ace8c05ec7d3683d27083c4f1e7e"
+    },
+    "futile.options": {
+      "Package": "futile.options",
+      "Version": "1.0.1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "0d9bf02413ddc2bbe8da9ce369dcdd2b"
+    },
     "future": {
       "Package": "future",
       "Version": "1.34.0",
@@ -1134,6 +1245,21 @@
       ],
       "Hash": "15e9634c0fcd294799e9b2e929ed1b86"
     },
+    "geometry": {
+      "Package": "geometry",
+      "Version": "0.5.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "Rcpp",
+        "RcppProgress",
+        "linprog",
+        "lpSolve",
+        "magic"
+      ],
+      "Hash": "b052bd270aeddeca332c20feecfb039d"
+    },
     "ggplot2": {
       "Package": "ggplot2",
       "Version": "3.5.1",
@@ -1189,6 +1315,19 @@
       ],
       "Hash": "66488692cb8621bc78df1b9b819497a6"
     },
+    "ggsci": {
+      "Package": "ggsci",
+      "Version": "3.2.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "ggplot2",
+        "grDevices",
+        "scales"
+      ],
+      "Hash": "0c3268cddf4d3a3ce4e7e6330f8e92c8"
+    },
     "globals": {
       "Package": "globals",
       "Version": "0.16.3",
@@ -1278,6 +1417,27 @@
       ],
       "Hash": "588d091c35389f1f4a9d533c8d709b35"
     },
+    "harmony": {
+      "Package": "harmony",
+      "Version": "1.2.1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "Matrix",
+        "R",
+        "Rcpp",
+        "RcppArmadillo",
+        "RcppProgress",
+        "RhpcBLASctl",
+        "cowplot",
+        "dplyr",
+        "ggplot2",
+        "methods",
+        "rlang",
+        "tibble"
+      ],
+      "Hash": "1baaf521d42483d6d36d5c2f425e1ad9"
+    },
     "here": {
       "Package": "here",
       "Version": "1.0.1",
@@ -1475,6 +1635,17 @@
       ],
       "Hash": "b64ec208ac5bc1852b285f665d6368b3"
     },
+    "lambda.r": {
+      "Package": "lambda.r",
+      "Version": "1.2.4",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "formatR"
+      ],
+      "Hash": "b1e925c4b9ffeb901bacf812cbe9a6ad"
+    },
     "later": {
       "Package": "later",
       "Version": "1.3.2",
@@ -1537,6 +1708,17 @@
       ],
       "Hash": "b8552d117e1b808b09a832f589b79035"
     },
+    "linprog": {
+      "Package": "linprog",
+      "Version": "0.9-4",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "lpSolve"
+      ],
+      "Hash": "66e9d4ebd71ddcd6f86a2a9a34f5cdc5"
+    },
     "listenv": {
       "Package": "listenv",
       "Version": "0.9.1",
@@ -1560,6 +1742,24 @@
       ],
       "Hash": "c6fafa6cccb1e1dfe7f7d122efd6e6a7"
     },
+    "lpSolve": {
+      "Package": "lpSolve",
+      "Version": "5.6.21",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "730a90bdc519fb0caff03df11218ddd8"
+    },
+    "magic": {
+      "Package": "magic",
+      "Version": "1.6-1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "abind"
+      ],
+      "Hash": "1da6217cea8a3ef496258819b80770e1"
+    },
     "magrittr": {
       "Package": "magrittr",
       "Version": "2.0.3",
@@ -1748,6 +1948,17 @@
       ],
       "Hash": "68a2d681e10cf72f0afa1d84d45380e5"
     },
+    "pdfCluster": {
+      "Package": "pdfCluster",
+      "Version": "1.0-4",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "geometry",
+        "methods"
+      ],
+      "Hash": "51e3a7a4af0b863e5d380575cbd33cda"
+    },
     "pillar": {
       "Package": "pillar",
       "Version": "1.9.0",
@@ -1899,6 +2110,30 @@
       ],
       "Hash": "017561f17632c065388b7062da030952"
     },
+    "rOpenScPCA": {
+      "Package": "rOpenScPCA",
+      "Version": "0.1.0",
+      "Source": "GitHub",
+      "RemoteType": "github",
+      "RemoteHost": "api.github.com",
+      "RemoteUsername": "AlexsLemonade",
+      "RemoteRepo": "OpenScPCA-analysis",
+      "RemoteSubdir": "packages/rOpenScPCA",
+      "RemoteRef": "main",
+      "RemoteSha": "a5c36235eff73530cf496c4d82715e33e79fc90e",
+      "Requirements": [
+        "BiocParallel",
+        "SingleCellExperiment",
+        "bluster",
+        "dplyr",
+        "methods",
+        "pdfCluster",
+        "purrr",
+        "tibble",
+        "tidyr"
+      ],
+      "Hash": "f320ea9842ac8f8eb77685aa3155751d"
+    },
     "rappdirs": {
       "Package": "rappdirs",
       "Version": "0.3.3",
@@ -2165,6 +2400,17 @@
       ],
       "Hash": "c956d93f6768a9789edbc13072b70c78"
     },
+    "snow": {
+      "Package": "snow",
+      "Version": "0.4-4",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "utils"
+      ],
+      "Hash": "40b74690debd20c57d93d8c246b305d4"
+    },
     "sourcetools": {
       "Package": "sourcetools",
       "Version": "0.1.7-1",

analyses/cell-type-nonETP-ALL-03/results/README.md

@@ -12,4 +12,8 @@ These are the generated outputs for each sample in the S3 bucket:
 -   `rds` objects: `s3://researcher-650251722463-us-east-2/cell-type-nonETP-ALL-03/results/rds`
 -   metadata and ScType results: `s3://researcher-650251722463-us-east-2/cell-type-nonETP-ALL-03/results/`
 -   CopyKat results: `s3://researcher-650251722463-us-east-2/cell-type-nonETP-ALL-03/results/copykat_output`
--   umap and dot plots: `s3://researcher-650251722463-us-east-2/cell-type-nonETP-ALL-03/plots` (are also found in the repository plots/).
+-   evaluating cluster separation, stability, and purity: `s3://researcher-650251722463-us-east-2/cell-type-nonETP-ALL-03/results/evalClus`
+-   umap and dot plots: `s3://researcher-650251722463-us-east-2/cell-type-nonETP-ALL-03/plots`
+-   violin and stacked bar plots for exploring the results of CopyKat prediction: `s3://researcher-650251722463-us-east-2/cell-type-nonETP-ALL-03/plots/copykat_exploration`
+
+\*\*All the plots are also found in the repository plots/.