Question: Issues with col2rgb
0
gravatar for anamaria
15 months ago by
anamaria100
anamaria100 wrote:

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 • 245 views
ADD COMMENTlink modified 15 months ago • written 15 months ago by anamaria100

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.

ADD REPLYlink written 15 months ago by Jean-Karim Heriche23k

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

ADD REPLYlink written 15 months ago by anamaria100
0
gravatar for anamaria
15 months ago by
anamaria100
anamaria100 wrote:

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

 dim1 in 1:2
ADD COMMENTlink written 15 months ago by anamaria100
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