X-Git-Url: https://git.arvados.org/lightning.git/blobdiff_plain/0a6b0ee247d7d9f46acc2147870be443a624442d..29666c930fc3f6f81edc7eb306c1cb2765e77c58:/plot.go

diff --git a/plot.go b/plot.go
index 1d80e8a21c..6deaff6fc7 100644
--- a/plot.go
+++ b/plot.go
@@ -5,16 +5,22 @@
 package lightning
 
 import (
+	_ "embed"
 	"flag"
 	"fmt"
 	"io"
 	_ "net/http/pprof"
+	"os/exec"
+	"strings"
 
 	"git.arvados.org/arvados.git/sdk/go/arvados"
 )
 
 type pythonPlot struct{}
 
+//go:embed plot.py
+var plotscript string
+
 func (cmd *pythonPlot) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
 	var err error
 	defer func() {
@@ -26,15 +32,24 @@ func (cmd *pythonPlot) RunCommand(prog string, args []string, stdin io.Reader, s
 	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")
-	colormapFilename := flags.String("colormap", "", "use first two columns of `colormap.csv` as id->color mapping")
+	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{
@@ -51,12 +66,40 @@ func (cmd *pythonPlot) RunCommand(prog string, args []string, stdin io.Reader, s
 			},
 		},
 	}
-	err = runner.TranslatePaths(inputFilename, sampleListFilename, colormapFilename)
-	if err != nil {
-		return 1
+	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(plotscript)
+		cmd.Stdout = stdout
+		cmd.Stderr = stderr
+		err = cmd.Run()
+		if err != nil {
+			return 1
+		}
+		return 0
 	}
 	runner.Prog = "python3"
-	runner.Args = []string{"/plot.py", *inputFilename, *sampleListFilename, *colormapFilename, "/mnt/output/plot.png"}
+	runner.Args = append([]string{"/plot.py"}, args...)
 	var output string
 	output, err = runner.Run()
 	if err != nil {
@@ -65,71 +108,3 @@ func (cmd *pythonPlot) RunCommand(prog string, args []string, stdin io.Reader, s
 	fmt.Fprintln(stdout, output+"/plot.png")
 	return 0
 }
-
-var plotscript = `
-import csv
-import os
-import os.path
-import scipy
-import sys
-
-infile = sys.argv[1]
-X = scipy.load(infile)
-
-colors = None
-if sys.argv[2]:
-    labels = {}
-    with open(sys.argv[2], 'rt') as samplelist:
-        for row in csv.reader(samplelist):
-            labels[row[1]] = '---'
-    with open(sys.argv[3], 'rt') as colormap:
-        for row in csv.reader(colormap):
-            ident=row[0]
-            label=row[1]
-            for fnm in labels:
-                if row[0] in fnm:
-                    labels[fnm] = row[1]
-    colors = []
-    labelcolors = {
-        'PUR': 'firebrick',
-        'CLM': 'firebrick',
-        'MXL': 'firebrick',
-        'PEL': 'firebrick',
-        'TSI': 'green',
-        'IBS': 'green',
-        'CEU': 'green',
-        'GBR': 'green',
-        'FIN': 'green',
-        'LWK': 'coral',
-        'MSL': 'coral',
-        'GWD': 'coral',
-        'YRI': 'coral',
-        'ESN': 'coral',
-        'ACB': 'coral',
-        'ASW': 'coral',
-        'KHV': 'royalblue',
-        'CDX': 'royalblue',
-        'CHS': 'royalblue',
-        'CHB': 'royalblue',
-        'JPT': 'royalblue',
-        'STU': 'blueviolet',
-        'ITU': 'blueviolet',
-        'BEB': 'blueviolet',
-        'GIH': 'blueviolet',
-        'PJL': 'blueviolet',
-    }
-    for fnm in sorted(labels.keys()):
-        if labels[fnm] in labelcolors:
-            colors.append(labelcolors[labels[fnm]])
-        else:
-            colors.append('black')
-
-from matplotlib.figure import Figure
-from matplotlib.patches import Polygon
-from matplotlib.backends.backend_agg import FigureCanvasAgg
-fig = Figure()
-ax = fig.add_subplot(111)
-ax.scatter(X[:,0], X[:,1], c=colors, s=60, marker='o', alpha=0.5)
-canvas = FigureCanvasAgg(fig)
-canvas.print_figure(sys.argv[4], dpi=80)
-`