Entering edit mode
15 months ago
franciscaelibethgalvez
▴
10
I've been making various heatmaps for different gene sets and I added the log2FoldChange values as an extra column, but I need to leave it as a barplot, but I've been lost on how to put those log2FoldChange values to appear as bars. Any help is appreciated, thanks ;)
ha <- HeatmapAnnotation(summary = anno_summary(gp = gpar(fill = 3),
height = unit(1, "cm")))
h1<- Heatmap(mat.scaled, cluster_rows = F, name="Z-score", cluster_columns = T, col= col_fun, width = ncol(mat.scaled)*unit(10, "mm"), height = nrow(mat.scaled)*unit(10, "mm"), show_column_names = F, show_column_dend = T, top_annotation=colAnn)
h2 <- Heatmap(l2_val, row_labels = df.top$symbol,
cluster_rows = F, name="LFC", rowAnnotation = ha, col = col_logFC,
cell_fun = function(j, i, x, y, w, h, col) { # add text to each grid
grid.text(round(l2_val[i, j],2), x, y)
}, rect_gp = gpar(col = "white", lwd = 0.09), width = ncol(mat.scaled)*unit(3, "mm"), height = nrow(mat.scaled)*unit(3, "mm"), show_column_names = F)
h<-h1+h2
hf<-draw(h, merge_legend = TRUE, column_dend_side = "bottom", ht_gap = unit(4.5, "mm"))
data:
baseMean log2FoldChange lfcSE stat
TRINITY_DN2981_c1_g1_i4 26.36635 6.257222 1.14626254 5.458804
TRINITY_DN973_c0_g2_i2 32.61071 2.947533 0.52482872 5.616181
TRINITY_DN46186_c0_g1_i1 1430.14501 2.730862 0.12740461 21.434559
TRINITY_DN8465_c0_g2_i1 37.13230 2.422529 0.51178737 4.733468
TRINITY_DN9419_c0_g1_i1 74.52868 1.733437 0.36643757 4.730512
TRINITY_DN1083_c0_g1_i2 37.94081 1.647859 0.53771139 3.064578
TRINITY_DN6777_c0_g4_i2 27.69262 1.600363 0.52835576 3.028951
TRINITY_DN652_c2_g1_i1 136.64937 1.222090 0.34789911 3.512773
TRINITY_DN6510_c0_g1_i2 111.16280 1.180603 0.26047578 4.532486
TRINITY_DN7412_c0_g4_i1 5949.81391 1.117412 0.09549244 11.701574
TRINITY_DN1563_c0_g1_i1 770.73847 -1.040489 0.14274078 -7.289363
TRINITY_DN6422_c0_g1_i1 760.51126 -1.269152 0.15454838 -8.212005
TRINITY_DN7939_c0_g1_i1 114.76486 -1.361774 0.26594654 -5.120479
TRINITY_DN2334_c2_g1_i2 244.69072 -1.580514 0.19002448 -8.317425
TRINITY_DN7742_c1_g4_i1 1078.44672 -1.589249 0.14274258 -11.133672
TRINITY_DN5417_c0_g1_i2 50.44834 -1.791680 0.37966640 -4.719091
TRINITY_DN1371_c0_g1_i3 584.55158 -2.228805 0.32975786 -6.758914
TRINITY_DN8762_c2_g2_i4 48.89964 -2.256699 0.39432833 -5.722894
TRINITY_DN1109_c1_g1_i1 3585.65418 -2.322378 0.09197339 -25.250536
TRINITY_DN118_c0_g1_i1 10670.24277 -2.457908 0.10578683 -23.234534
TRINITY_DN865_c1_g1_i9 1214.23519 -2.580990 0.13942780 -18.511300
TRINITY_DN16132_c0_g2_i1 22.87642 -2.655935 0.61338410 -4.329971
TRINITY_DN899_c0_g1_i2 314.85164 -2.902132 0.41458428 -7.000101
TRINITY_DN3169_c0_g1_i1 1171.46366 -3.903238 0.15413663 -25.323231
TRINITY_DN319_c0_g1_i2 3928.38869 -4.565373 0.12861494 -35.496442
pvalue padj symbol
TRINITY_DN2981_c1_g1_i4 4.793529e-08 1.713703e-06 psbP_3
TRINITY_DN973_c0_g2_i2 1.952238e-08 7.375347e-07 psaA
TRINITY_DN46186_c0_g1_i1 6.363366e-102 7.767245e-99 rbcS
TRINITY_DN8465_c0_g2_i1 2.207157e-06 5.835592e-05 petB
TRINITY_DN9419_c0_g1_i1 2.239542e-06 5.915114e-05 petA
TRINITY_DN1083_c0_g1_i2 2.179771e-03 2.456542e-02 petD
TRINITY_DN6777_c0_g4_i2 2.454048e-03 2.692835e-02 atpE
TRINITY_DN652_c2_g1_i1 4.434570e-04 6.503764e-03 psbL
TRINITY_DN6510_c0_g1_i2 5.829360e-06 1.400412e-04 psbA
TRINITY_DN7412_c0_g4_i1 1.251114e-31 2.876215e-29 ChIl
TRINITY_DN1563_c0_g1_i1 3.114234e-13 2.125889e-11 LHCB_3
TRINITY_DN6422_c0_g1_i1 2.175251e-16 1.939416e-14 LHCA1
TRINITY_DN7939_c0_g1_i1 3.047603e-07 9.468996e-06 psbP_1
TRINITY_DN2334_c2_g1_i2 8.989518e-17 8.288788e-15 LHC2
TRINITY_DN7742_c1_g4_i1 8.601759e-29 1.763911e-26 TRX-F
TRINITY_DN5417_c0_g1_i2 2.369004e-06 6.218604e-05 psbP_2
TRINITY_DN1371_c0_g1_i3 1.390299e-11 7.990478e-10 LHCB1
TRINITY_DN8762_c2_g2_i4 1.047246e-08 4.110881e-07 psaL
TRINITY_DN1109_c1_g1_i1 1.117313e-140 1.975178e-137 LHCB_2
TRINITY_DN118_c0_g1_i1 2.039227e-119 3.074794e-116 LHCB_1
TRINITY_DN865_c1_g1_i9 1.674102e-76 1.362294e-73 FER
TRINITY_DN16132_c0_g2_i1 1.491292e-05 3.257887e-04 psbS
TRINITY_DN899_c0_g1_i2 2.557783e-12 1.591351e-10 ELIP2
TRINITY_DN3169_c0_g1_i1 1.772556e-141 3.245424e-138 CBR
TRINITY_DN319_c0_g1_i2 5.577636e-276 1.429715e-271 LHCSR1
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