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generation of heat map by excel data.

data i have a gene along with there p-value from different treatments. how to find out the common gene with there p-values from gene data and make heat map with that data .

r excel heatmap
• 4,930 views • link
updated by Ram Ram • written by abhilashreddy495 • abhilashreddy495

Please provide example input data, and expected output.

• 1 views • link
written by zx8754 zx8754

Try brbarraytools excel plug in

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written by cpad0112 cpad0112 
231N VS 231T            231N VS 231C            231T VS 231C    
Gene    PValue      Gene    PValue      Gene    PValue
CCL20   2.59254E-07     GABRE   2.23694E-10     NEDD9   1.65267E-13
IL1B    1.49732E-06     FER1L4  2.67623E-09     PPL 2.03797E-13
SBSN    3.30121E-06     CEMIP   2.85536E-09     FER1L4  1.42883E-12
SERPINB2    5.01643E-06     PPL 2.04863E-08     FLJ22447    5.28781E-12
NGFR    8.20017E-06     NEDD9   5.11885E-08     DHRS3   2.31982E-10
AL512488.1  1.61845E-05     NEAT1   9.62719E-08     ADGRF1  1.18121E-09
            PDE4B   1.62611E-07     RASD2   1.66557E-09
            FLJ22447    1.79007E-07     CEMIP   2.0201E-09
            ZNF608  7.63326E-07     INHBA   2.16685E-08
            SPINK4  7.73203E-07     AL591845.1  4.66631E-08
            ADGRF1  1.0283E-06      CLIC3   4.91309E-08
            DAPK2   1.04759E-06     NEAT1   8.02813E-08
            ZBED6CL 1.33771E-06     SEMA3B  1.97286E-07
            ZNF334  1.61097E-06     ZNF608  2.131E-07
            AC037198.2  1.93544E-06     THBS1   2.3134E-07
            AC015813.1  1.97652E-06     RNF43   2.99691E-07
            FILIP1L 3.71662E-06     MUC1    3.42552E-07
            DHRS3   4.08434E-06     PDGFRB  3.70966E-07
            FP236383.3  4.65843E-06     GYG2    3.85315E-07
            CCDC146 7.01828E-06     ZNF334  5.06024E-07
            FAT4    8.46845E-06     C4orf26 5.52401E-07
            SLC25A27    1.00856E-05     PBX1    5.93494E-07
            MIR3142HG   1.12587E-05     SEC31B  6.53884E-07
            TNS4    1.16045E-05     FOXQ1   8.67299E-07
            ZNF117  1.43947E-05     FBLN7   8.879E-07
            PPFIA4  1.91171E-05     PLEKHA7 1.11565E-06
            MATN2   2.01297E-05     COL5A1  1.12397E-06
            PBX1    2.07263E-05     EFEMP2  1.28677E-06
            CPA4    3.00126E-05     PPFIA4  1.43957E-06
            AL591845.1  3.14543E-05     ZBED6CL 1.44446E-06
            SEC31B  3.44318E-05     CST6    2.78727E-06
            PTGS1   4.25242E-05     SNHG18  3.07328E-06
            GLCCI1  4.46737E-05     FILIP1L 3.43167E-06
            SNHG18  5.34757E-05     SAA2    3.54419E-06
            CCNG2   5.62871E-05     FP236383.3  5.46834E-06
            EDIL3   6.33234E-05     ELF3    6.77953E-06
            PROM2   6.53123E-05     SPINT1  6.83334E-06
            FOXQ1   6.62362E-05     MATN2   6.92468E-06
            BMF 6.65339E-05     CCDC146 7.17387E-06
            RNF43   7.85292E-05     ZNF117  7.74943E-06
            SPACA6  8.36892E-05     SERINC2 8.02637E-06
            ZNF493  0.000110459     TMEM25  9.37832E-06
            AP005233.2  0.000111489     GGT1    1.19989E-05
            ABCC3   0.000116345     LOXL4   1.25495E-05
            KLHDC1  0.000120487     GRB7    1.36431E-05
            TTLL3   0.000123342     JCAD    1.48539E-05
            DNAH11  0.000134317     PMEPA1  1.51491E-05
            KCNMB4  0.000144215     C1R 1.71287E-05
            PDE7B   0.000166044     PDE7B   1.77777E-05
            RARRES2 0.000181946     ICAM5   1.77864E-05
            AC004656.1  0.000182757     TTLL3   2.00604E-05
            SLC2A10 0.000188719     FAT4    2.01584E-05
            CPS1    0.000192623     TACSTD2 2.01768E-05
            MB  0.000195986     MDGA1   2.02132E-05
            PARD6B  0.000225652     PDZK1IP1    2.06739E-05
            NRIP1   0.000233619     CXCR4   2.17145E-05
            STS 0.000233708     SPOCD1  2.19388E-05
            LINC01411   0.000236023     AF121898.1  2.22151E-05
            FAT3    0.000236122     SLC2A10 2.33106E-05
• 1 views • link
updated by Ram Ram • written by abhilashreddy495 • abhilashreddy495

Forgive me, my friend, but very few people will help you if you paste data in that way and leave a lot of work to others to tidy it up. We are volunteers here and [mostly] have full-time study or employment. If you want to upload your file somewhere and provide a link, that may be better.

Also, it is not recommended to use Excel for 'analysis' in bioinformatics. Formats should be plain-text an well-structured for easy parsing with command-line programs/functions, such as TSV, CSV, JSon, etc.

• 1 views • link
written by Kevin Blighe Kevin Blighe

From the screeshots, it is evident that you are already using Rstudio (thus R). R has excellent packages for heatmaps. Refer to Kevin Blighe's excellent tutorial/posts on heatmaps.

• 1 views • link
written by cpad0112 cpad0112

if your data is already in R, then it is most helpful to provide the dput() output of a small selection of the data (head()), something like this:

dput(head(df))

then copy/paste this output. This allows others to recreate the exact R object you are working with.

• 1 views • link
written by steve steve

Also you can look at ggplot2 for this, cheatsheet here, particularly look at geom_tile function. However you will need to use something like reshape2 to convert your dataframe to 'long' format, description here

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written by steve steve

a third comment; it looks like the Excel sheet you are trying to import has 2-line headers. Your best bet is to clean this up in Excel prior to importing, to make the headers 1-line only. Or you can try to wrangle it in R

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written by steve steve

Please click on "edit" link and paste your data as text, not image.

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written by zx8754 zx8754

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