Issues with col2rgb
1
0
Entering edit mode
5.1 years ago
anamaria ▴ 220

Hi,

this is my data and code:

> rownames(cc)
 [1] "DwoC_2318_30mM"  "DwoC_3395_30mM"  "DwoC_6154_30mM"  "DwoC_16362_30mM"
 [5] "DwoC_18296_30mM" "DwoC_21183_30mM" "DwoC_25224_30mM" "DwC_1026_30mM"  
 [9] "DwC_6009_30mM"   "DwC_11167_30mM"  "DwC_13206_30mM"  "DwC_17075_30mM" 
[13] "DwC_21127_30mM"  "DwC_26008_30mM"  "DwC_27141_30mM"  "NoD_7012_30mM"  
[17] "NoD_7344_30mM"   "NoD_11985_30mM"  "NoD_14381_30mM"  "NoD_14520_30mM" 
[21] "NoD_14569_30mM"  "NoD_14581_30mM" 
> mds <- cc %>% dist() %>% cmdscale(k=3)
> mds <- cc %>% dist() %>% cmdscale(k=3) %>% as_tibble()
> mds$cols <- as.factor(c(rep("nPDR.hg",8),  rep("PDR.hg",7),  rep("NoD.hg",7))) 
> pdf(file = "MDS_gene_expression_new_reduced_HG.pdf")
> 
> 
>                     for (dim1 in 1:3){
+                     for (dim2 in (dim1+1):3){
+                         d1 = paste0("Dim.",dim1); d2 = paste0("Dim.",dim2)
+                         colnames(mds)[c(dim1,dim2)] <- c(d1,d2)
+                         print(ggscatter(mds, x = d1, y = d2, color = "cols",size=3 ,palette=c("blue","red","yellow")))
+                     }
 +                 }
  Error in grDevices::col2rgb(colour, TRUE) : invalid color name 'cols'
> dev.off()

Does anyone know why I am getting this Error?

> head(mds)
# A tibble: 6 x 4
       V1    V2     V3 cols   
    <dbl> <dbl>  <dbl> <fct>  
1   2.97  -5.92  2.56  nPDR.hg
2  -0.323 -4.95  1.77  nPDR.hg
3 -11.8   -5.20 -3.83  nPDR.hg
4  -1.85   3.87 -0.271 nPDR.hg
5   2.34  -6.91  2.42  nPDR.hg
6  -4.81  -6.85  0.952 nPDR.hg

Thanks Ana

R • 889 views
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Entering edit mode

Try removing the quotes around cols. In ggplot2, this is meant to refer to the cols column of the data frame containing the data. By the way this is a question for StackOverflow since it's about R programming.

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HI, I tried color = cols but again the same error.

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Entering edit mode
5.1 years ago
anamaria ▴ 220

it was wrong dimension in the loop, it should be:

 dim1 in 1:2
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