Question: Issues with col2rgb
0
gravatar for anamaria
5 months ago by
anamaria80
anamaria80 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 • 153 views
ADD COMMENTlink modified 5 months ago • written 5 months ago by anamaria80

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 5 months ago by Jean-Karim Heriche21k

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

ADD REPLYlink written 5 months ago by anamaria80
0
gravatar for anamaria
5 months ago by
anamaria80
anamaria80 wrote:

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

 dim1 in 1:2
ADD COMMENTlink written 5 months ago by anamaria80
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