Pheatmap x must be numeric
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Entering edit mode
15 months ago
Hamza ▴ 10

I receive the following error from pheatmap:

pheatmap(my_matrix,annotation_col = my_metadata)
Error in cut.default(a, breaks = 100) : 'x' must be numeric

However, my matrix is already numeric

apply(my_matrix,2,is.numeric)

      GCBGE0767G POHRZ1835F ZCBZP7326X HHMJY1357N IMTWE9463H DJPSO3322R REXYQ6498S OFCFL1180G KTGMI0703N AQDZN3914I IBKRI1023I HGIIC0255O PEUMK2767Q 
          TRUE       TRUE       TRUE       TRUE       TRUE       TRUE       TRUE       TRUE       TRUE       TRUE       TRUE       TRUE       TRUE 
    IZTMF7642U MXKMR5399Y BLBGG0808F PGHVS1628Y DTOJM9017I FOTAV7788Y IDWVU4461M YBECA7334K EGTWK7592T EVDMU2971O LIDGN5172P YKFAX1349I YLOXV4155S 
          TRUE       TRUE       TRUE       TRUE       TRUE       TRUE       TRUE       TRUE       TRUE       TRUE       TRUE       TRUE       TRUE 
    PBUNH9938W CCAUS4102V MGELH2280E BCZST1456Y ZLYRP8159V UKXJB6887Z YANQL8585B WUMUL4815C WTXQA4810I WOKDQ1603L YLNGA5107D WJRIA0010K ACNVG9218A 
          TRUE       TRUE       TRUE       TRUE       TRUE       TRUE       TRUE       TRUE       TRUE       TRUE       TRUE       TRUE       TRUE 
    AUGTB9564V FVQNA3298H UGBZX9149O VHPPI3077E KQKYD2822Z UERHW1594Z VKXDZ2923H BBKEX8083N UAHTX3652M HQVUP0102D GHKCR0738E XLHDC1857Z FKLBX7676A 
          TRUE       TRUE       TRUE       TRUE       TRUE       TRUE       TRUE       TRUE       TRUE       TRUE       TRUE       TRUE       TRUE 
    SZHNM3174B 
          TRUE

So I don't understand the issue. Can anyone take a guess?

class(my_matrix)
[1] "matrix, array"

My matrix looks like this

                        GCBGE0767G POHRZ1835F ZCBZP7326X HHMJY1357N IMTWE9463H DJPSO3322R REXYQ6498S OFCFL1180G KTGMI0703N AQDZN3914I IBKRI1023I
A2M                      13.328123  14.177430  13.215992  14.259884  14.106684  12.668580  13.841886  14.203813  14.041668  13.496955  12.869849
A2ML1                     8.939902   8.550417   8.309676   6.091018  11.837218  11.466685   8.694179   9.014055   9.832503   5.828606   5.597503
A4GALT                   10.405861  10.703880  10.477482  10.346346   8.780233   8.854969   8.925953   9.471257  10.937927   8.338915   7.453108
AAAS                     11.397697  11.037208  10.840574  10.505638  10.943570  11.186013  10.936939  10.780347  10.988737  11.139503  11.102039
AACS                      9.967724  10.075644   9.361871   8.563242   9.334040   9.299174   9.835727   9.999253   9.319627  10.168981  10.529605
AADAC                     4.128528   5.384454   4.128528   6.730545   4.438229   4.476618   5.956244   5.617084   5.249543   7.579926   4.128528
deseq2 r pheatmap • 601 views
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Entering edit mode

Please try as.matrix(my_matrix) or data.matrix(my_matrix). Also, please ensure that the colnames of my_matrix are the same as the rownames of my_metadata

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