19526: Add manhattan plot.

[lightning.git] / pca_plot.go

diff --git a/pca_plot.go b/pca_plot.go
new file mode 100644 (file)
index 0000000..88ba06c
--- /dev/null
+++ b/pca_plot.go
@@ -0,0 +1,109 @@
+// Copyright (C) The Lightning Authors. All rights reserved.
+//
+// SPDX-License-Identifier: AGPL-3.0
+
+package lightning
+
+import (
+       _ "embed"
+       "flag"
+       "fmt"
+       "io"
+       "os/exec"
+       "strings"
+
+       "git.arvados.org/arvados.git/sdk/go/arvados"
+)
+
+type pythonPlot struct{}
+
+//go:embed pca_plot.py
+var pcaPlotPy string
+
+func (cmd *pythonPlot) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
+       var err error
+       defer func() {
+               if err != nil {
+                       fmt.Fprintf(stderr, "%s\n", err)
+               }
+       }()
+       flags := flag.NewFlagSet("", flag.ContinueOnError)
+       flags.SetOutput(stderr)
+       projectUUID := flags.String("project", "", "project `UUID` for output data")
+       inputFilename := flags.String("i", "-", "input `file`")
+       outputFilename := flags.String("o", "", "output `filename` (e.g., './plot.png')")
+       sampleListFilename := flags.String("samples", "", "use second column of `samples.csv` as complete list of sample IDs")
+       phenotypeFilename := flags.String("phenotype", "", "use `phenotype.csv` as id->phenotype mapping (column 0 is sample id)")
+       cat1Column := flags.Int("phenotype-cat1-column", 1, "0-based column `index` of 1st category in phenotype.csv file")
+       cat2Column := flags.Int("phenotype-cat2-column", -1, "0-based column `index` of 2nd category in phenotype.csv file")
+       xComponent := flags.Int("x", 1, "1-based PCA component to plot on x axis")
+       yComponent := flags.Int("y", 2, "1-based PCA component to plot on y axis")
+       priority := flags.Int("priority", 500, "container request priority")
+       runlocal := flags.Bool("local", false, "run on local host (default: run in an arvados container)")
+       err = flags.Parse(args)
+       if err == flag.ErrHelp {
+               err = nil
+               return 0
+       } else if err != nil {
+               return 2
+       } else if flags.NArg() > 0 {
+               err = fmt.Errorf("errant command line arguments after parsed flags: %v", flags.Args())
+               return 2
+       }
+
+       runner := arvadosContainerRunner{
+               Name:        "lightning pca-plot",
+               Client:      arvados.NewClientFromEnv(),
+               ProjectUUID: *projectUUID,
+               RAM:         4 << 30,
+               VCPUs:       1,
+               Priority:    *priority,
+               Mounts: map[string]map[string]interface{}{
+                       "/pca_plot.py": map[string]interface{}{
+                               "kind":    "text",
+                               "content": pcaPlotPy,
+                       },
+               },
+       }
+       if !*runlocal {
+               err = runner.TranslatePaths(inputFilename, sampleListFilename, phenotypeFilename)
+               if err != nil {
+                       return 1
+               }
+               *outputFilename = "/mnt/output/plot.png"
+       }
+       args = []string{
+               *inputFilename,
+               fmt.Sprintf("%d", *xComponent),
+               fmt.Sprintf("%d", *yComponent),
+               *sampleListFilename,
+               *phenotypeFilename,
+               fmt.Sprintf("%d", *cat1Column),
+               fmt.Sprintf("%d", *cat2Column),
+               *outputFilename,
+       }
+       if *runlocal {
+               if *outputFilename == "" {
+                       fmt.Fprintln(stderr, "error: must specify -o filename.png in local mode (or try -help)")
+                       return 1
+               }
+               cmd := exec.Command("python3", append([]string{"-"}, args...)...)
+               cmd.Stdin = strings.NewReader(pcaPlotPy)
+               cmd.Stdout = stdout
+               cmd.Stderr = stderr
+               err = cmd.Run()
+               if err != nil {
+                       return 1
+               }
+               return 0
+       }
+       runner.Prog = "python3"
+       runner.Args = append([]string{"/pca_plot.py"}, args...)
+       var output string
+       output, err = runner.Run()
+       if err != nil {
+               return 1
+       }
+       fmt.Fprintln(stdout, output+"/plot.png")
+       return 0
+}