Merge branch '19524-pca'

[lightning.git] / plot.go

diff --git a/plot.go b/plot.go
index 9959b5067c09d42ee671162a8f04729702278ffe..98b7eece27ae48e5c15166ddae70c662f6c7cf3c 100644 (file)
--- a/plot.go
+++ b/plot.go
@@ -35,8 +35,10 @@ func (cmd *pythonPlot) RunCommand(prog string, args []string, stdin io.Reader, s
        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)")
-       phenotypeCategoryColumn := flags.Int("phenotype-category-column", -1, "0-based column `index` of 2nd category in phenotype.csv file")
-       phenotypeColumn := flags.Int("phenotype-column", 1, "0-based column `index` of phenotype in phenotype.csv file")
+       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)
@@ -68,7 +70,16 @@ func (cmd *pythonPlot) RunCommand(prog string, args []string, stdin io.Reader, s
                }
                *outputFilename = "/mnt/output/plot.png"
        }
-       args = []string{*inputFilename, *sampleListFilename, *phenotypeFilename, fmt.Sprintf("%d", *phenotypeCategoryColumn), fmt.Sprintf("%d", *phenotypeColumn), *outputFilename}
+       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)")