search

bmansfeld / QTLseqr

QTLseqr is an R package for QTL mapping using NGS Bulk Segregant Analysis
65 stars 42 forks source link

The script running normal and no error produced, why no plot generated? just only produce a table of CSV #44

Closed haohui123 closed 3 years ago

haohui123 commented 3 years ago

Help my QTLseqr was installed in linux R envs, R was installed use anconda, the QTLseqr installed success, but when running my script, though no error produced, but the Rplots.pdf and df had nothing! Has anyone meet this situation?

plotQTLStats(

  • SNPset = df_filt,
  • var = "Gprime",
  • plotThreshold = TRUE,
  • q = 0.01
  • ) plotQTLStats(
  • SNPset = df_filt,
  • var = "deltaSNP",
  • plotIntervals = TRUE) getQTLTable(
  • SNPset = df_filt,
  • alpha = 0.01,
  • export = TRUE,
  • fileName = "my_BSA_QTL1.csv"
  • ) CHROM qtl start end length nSNPs avgSNPs_Mb peakDeltaSNP 1 R05 1 2404 2923609 2921205 1689 578 0.3715301 2 R08 2 356332 3308448 2952116 316 107 0.5995971 3 R08 3 5518535 21451977 15933442 2755 173 0.6366040 4 R08 4 27354643 27493493 138850 4 29 0.3348856 posPeakDeltaSNP avgDeltaSNP maxGprime posMaxGprime meanGprime sdGprime 1 1892524 0.3606035 17.80104 1892524 16.34035 1.059533 2 3027509 0.4555751 19.03438 1280127 17.04648 1.551114 3 6880353 0.4669769 32.52107 6885361 22.81858 3.327091 4 27493493 0.2800255 19.11753 27493493 16.10660 2.012530 AUCaT meanPval meanQval 1 5917302 0.0002306070 0.006173703 2 7621865 0.0001949842 0.005554059 3 147785964 0.0000461582 0.002235581 4 381450 0.0002735495 0.006789872
bmansfeld commented 3 years ago

try something like this to save your plot

# Print the plot to a pdf file
pdf("myplot.pdf")
myplot <- plotQTLStats(paramaters.....)
print(myplot)
dev.off()