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3.2 years ago
aranyak111
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I am working with a zebrafish dataset with the following columns.
geneid baseMean log2FoldChange lfcSE stat pvalue padj mir99-1 mir99-2 mir99-3 KDR1 KDR2 KDR3 genename
ENSDARG00000087345 568.9632183 -6.20E+00 2.53E-01 -24.52506073 7.98E-133 1.39E-128 1184.991259 1155.817701 1040.461126 11.89199391 12.79560554 7.821623872 CABZ01059415.2
ENSDARG00000058371 2137.227454 -1.90E+00 1.23E-01 -15.45919908 6.54E-54 5.68E-50 3567.150951 3403.840003 3190.479638 928.7647244 838.1121628 895.0172459 krt5
ENSDARG00000026403 105.7002429 5.94E+00 3.91E-01 15.20933627 3.07E-52 1.77E-48 0.761073384 0 0.803444885 198.5962983 222.8567965 211.1838445 hephl1b
ENSDARG00000006427 307.5980773 -2.56E+00 1.69E-01 -15.1717102 5.44E-52 2.36E-48 571.5661114 502.4356798 515.8116161 84.43315677 85.30403692 86.03786259 fabp2
ENSDARG00000041381 211.673776 2.42E+00 1.77E-01 13.63946377 2.33E-42 8.10E-39 61.64694411 63.6131011 65.88248056 376.976207 345.4813495 356.4425736 arntl2
ENSDARG00000071601 644.7786927 -1.86E+00 1.46E-01 -12.6956589 6.25E-37 1.81E-33 1041.148389 1025.356935 983.4165391 229.5154825 295.3652278 293.8695826 pvalb9
ENSDARG00000054191 248.1707973 -2.73E+00 2.19E-01 -12.46919936 1.10E-35 2.73E-32 340.1998027 445.2917077 524.6495098 44.00037747 53.31502308 81.56836323 pgk1
ENSDARG00000098488 72.01580105 3.62E+00 2.96E-01 12.21415025 2.61E-34 5.67E-31 8.371807225 9.703693388 7.231003964 137.9471294 149.2820646 119.5591078 CABZ01118154.1
ENSDARG00000076129 134.0475054 2.89E+00 2.43E-01 11.89891469 1.20E-32 2.31E-29 14.4603943 42.04933801 30.53090563 241.4074764 236.7187025 239.1182155 si:dkey-108k21.17
ENSDARG00000035438 93.57767025 -3.06E+00 2.64E-01 -11.60017379 4.11E-31 7.14E-28 153.7368236 185.4483625 171.1337605 11.89199391 20.25970877 18.99537226 myhc4
ENSDARG00000010155 279.06936 1.87E+00 1.62E-01 11.54358934 7.95E-31 1.26E-27 107.3113472 115.3661325 126.9442918 468.5445601 436.1168888 420.1329394 abi1a
ENSDARG00000090039 98.78012873 -3.49E+00 3.04E-01 -11.47419245 1.78E-30 2.57E-27 128.6214019 174.666481 252.2816939 10.70279452 8.530403692 17.87799742 reck
ENSDARG00000061547 437.8935997 2.41E+00 2.16E-01 11.13186813 8.78E-29 1.17E-25 82.19592548 109.9751917 195.237107 727.7900273 762.40483 749.7585168 zgc:153409
ENSDARG00000035835 168.2611865 -2.43E+00 2.27E-01 -10.69600198 1.06E-26 1.32E-23 224.5166483 315.9091292 323.7882886 32.10838356 61.84542677 51.39924259 eef2k
ENSDARG00000103760 43.77828583 -4.51E+00 4.23E-01 -10.64650999 1.81E-26 2.10E-23 98.17846654 85.17686418 77.13070895 0 1.066300462 1.117374839 cfhl2
ENSDARG00000094300 162.8101355 -2.46E+00 2.32E-01 -10.61569008 2.52E-26 2.57E-23 306.7125738 264.1560978 268.3505916 23.78398782 49.04982123 64.80774065 NUPR1L
ENSDARG00000101393 196.2144366 -2.00E+00 1.89E-01 -10.62105025 2.38E-26 2.57E-23 344.766243 301.8926832 305.3090563 79.6763592 85.30403692 60.3382413 C6H17orf67
ENSDARG00000026369 559.9441682 -1.62E+00 1.53E-01 -10.53029815 6.26E-26 6.04E-23 881.3229787 852.8468299 816.3000031 217.6234886 293.2326269 298.339082 dbi
ENSDARG00000053990 1908.631378 -1.80E+00 1.72E-01 -10.47582276 1.12E-25 1.02E-22 2722.359495 2682.532128 3564.884954 614.8160852 908.4879932 958.7076117 hmgb2b
ENSDARG00000097615 81.17388891 -2.75E+00 2.65E-01 -10.40897787 2.26E-25 1.93E-22 139.2764293 141.2426482 151.8510832 13.0811933 18.12710785 23.46487161 si:ch211-108d22.2
ENSDARG00000100854 153.9825875 1.99E+00 1.91E-01 10.40561763 2.34E-25 1.93E-22 55.55835704 53.90940771 68.29281522 249.7318721 250.5806085 245.8224645 ago4
ENSDARG00000088330 2277.868137 -1.40E+00 1.36E-01 -10.24819681 1.21E-24 9.52E-22 3229.234369 3438.342024 3284.482689 1035.79267 1355.267887 1324.089184 si:ch211-5k11.2
ENSDARG00000052652 272.3044535 -1.77E+00 1.75E-01 -10.10878024 5.05E-24 3.81E-21 420.112508 368.7403487 486.0841554 105.8387458 129.0223558 124.0286071 fermt1
ENSDARG00000035326 83.09159923 -2.60E+00 2.58E-01 -10.0456011 9.61E-24 6.80E-21 166.6750711 131.5389548 137.3890753 21.40558904 19.19340831 22.34749678 nccrp1
ENSDARG00000035990 273.2937519 1.67E+00 1.66E-01 10.04368368 9.79E-24 6.80E-21 117.2053011 132.617143 132.568406 466.1661613 371.0725606 420.1329394 cited4a
ENSDARG00000001014 405.5070749 1.71E+00 1.71E-01 9.987688328 1.73E-23 1.15E-20 143.0817962 182.2137981 228.9817922 612.4376864 622.7194695 643.6079072 myh9b
ENSDARG00000017261 101.9226375 -2.58E+00 2.62E-01 -9.8202851 9.21E-23 5.71E-20 176.5690251 168.1973521 189.6129928 9.513595128 34.12161477 33.52124516 gdpd1
ENSDARG00000097601 49.84170742 -3.33E+00 3.39E-01 -9.822498879 9.01E-23 5.71E-20 93.61202624 85.17686418 101.2340555 4.756797564 5.331502308 8.93899871 dnajb9b
ENSDARG00000003641 232.8497019 -1.74E+00 1.77E-01 -9.789899787 1.24E-22 7.45E-20 383.5809856 324.5346344 376.0122061 88.00075494 108.7626471 116.2069832 tfg
I want to make the heatmap of the top 20 genes but instead of having Ensembl gene ids in the heatmap. I want to label the heatmap with the genename. The code to generate the heatmap is as follows.
library(pheatmap)
heatmap.data <- counts(dds)[topGenes,]
pheatmap(mat = heatmap.data)
pheatmap(mat = heatmap.data, scale = 'row')
colorScale <- colorRampPalette(c('navy','white','firebrick3'))
colorScale(30)
pheatmap(mat = heatmap.data, scale = 'row',
color = colorScale(30),
border_color = 'white',
fontsize_col = 7,
fontsize_row = 7,
cluster_col = F, filename='ag2598_2wk_heatmap.png')
refer to
labels_rowfunction.Exactly as cpad said, use
labels_rowargument within the pheatmap function to specify the column of the dataframe (genename) to use to label the rows of the heatmap. See?pheatmapfor more information.What is the question ?
I want to make the heatmap of the top 20 genes but instead of having Ensembl gene ids in the heatmap. I want to label the heatmap with the genename. The code to generate the heatmap is as follows. How to go about it?