<p>I'm clustering genes in terms of expression after clustering them. I'm taking out clusters and trying to find out what kind of GO terms are coming up. I came across this figure from this <a href="http://www.jimmunol.org/content/198/6/2238" rel="nofollow noreferrer">paper</a>, I want to do as the figure B:<a href="https://i.sstatic.net/igawg.jpg" rel="nofollow noreferrer"><img src="https://i.sstatic.net/igawg.jpg" alt="the second figure"></a></p>

<p><a href="https://drive.google.com/open?id=1YO7FOlZ7VG1ZSvWXaa1_L1rgoVCn-QLc" rel="nofollow noreferrer">Here</a> you can find the file I intend to use to make something like the above plot. </p>

<p>I am using this the code from <a href="https://www.biostars.org/p/299161/" rel="nofollow noreferrer">a question in Biostar</a>:</p>

<pre><code>DAVIDfile &lt;- "DAVID.txt"
DAVID &lt;- read.table(DAVIDfile, sep="\t", header=TRUE)
colnames(DAVID)
class(DAVID)

enrichBcutoff &lt;- 0.05
DAVID &lt;- subset(DAVID, Benjamini&lt; enrichBcutoff)
DAVID &lt;- DAVID[,c(1,2,3,5,6,10)]

head(DAVID)

A &lt;- data.frame(sigGeneList)

annGSEA &lt;- data.frame(row.names=A)
for (j in 1:length(sigGeneList))
{
  gene &lt;- sigGeneList[j]
  pattern &lt;- paste("^", gene, ", |, ", gene, "<span class="math-container">$| ", gene, ",", sep="")
    for (k in 1:nrow(DAVID))
  {
    if (any(grepl(pattern, DAVID$</span>Genes[k])))
    {
      annGSEA[j,k] &lt;- 1
    }
    else
    {
      annGSEA[j,k] &lt;- 0
    }
  }
}
colnames(annGSEA) &lt;- DAVID[,2]

annGSEA &lt;- annGSEA[,apply(annGSEA, 2, mean)!=0]

annGSEA &lt;- annGSEA[apply(annGSEA, 1, mean)!=0,]


require(ComplexHeatmap)
require(circlize)

topTable &lt;- topTable[which(topTable<span class="math-container">$Gene %in% rownames(annGSEA)),]
topTable &lt;- topTable[match(rownames(annGSEA), topTable$</span>Gene),]

geneLab=10
termLab=8

#Create heatmap annotations
dfMinusLog10FDRGenes &lt;- data.frame(-log10(topTable[which(topTable[,1] %in% rownames(annGSEA)),"padj"]))
dfMinusLog10FDRGenes[dfMinusLog10FDRGenes=="Inf"] &lt;- 0
dfFoldChangeGenes &lt;- data.frame(topTable[which(topTable[,1] %in% rownames(annGSEA)),"log2FoldChange"])
dfGeneAnno &lt;- data.frame(dfMinusLog10FDRGenes, dfFoldChangeGenes)
colnames(dfGeneAnno) &lt;- c("DEG\nsignificance\nscore", "Regulation")
dfGeneAnno[,2] &lt;- ifelse(dfGeneAnno[,2]&gt;0, "Up-regulated", "Down-regulated")
colours &lt;- list("Regulation"=c("Up-regulated"="royalblue", "Down-regulated"="yellow"))
haGenes &lt;- rowAnnotation(df=dfGeneAnno, col=colours, width=unit(1,"cm"))

dfMinusLog10BenjaminiTerms &lt;- data.frame(-log10(read.table(DAVIDfile, sep="\t", header=TRUE)[which(read.table(DAVIDfile, sep="\t", header=TRUE)$Term %in% colnames(annGSEA)),"Benjamini"]))
colnames(dfMinusLog10BenjaminiTerms) &lt;- "GO Term\nsignificance\nscore"
haTerms &lt;- HeatmapAnnotation(df=dfMinusLog10BenjaminiTerms,
                             colname=anno_text(colnames(annGSEA), rot=40, just="right", offset=unit(1,"npc")-unit(2,"mm"), gp=gpar(fontsize=termLab)),
                             annotation_height=unit.c(unit(1, "cm"), unit(8, "cm")))

pdf("GO.pdf", width=7, height=12)
hmapGSEA &lt;- Heatmap(annGSEA,

                    name="My enrichment",

                    split=dfGeneAnno[,2],

                    col=c("0"="white", "1"="forestgreen"),

                    rect_gp=gpar(col="grey85"),

                    cluster_rows=T,
                    show_row_dend=T,
                    row_title="Statistically-significant genes",
                    row_title_side="left",
                    row_title_gp=gpar(fontsize=12, fontface="bold"),
                    row_title_rot=0,
                    show_row_names=TRUE,
                    row_names_gp=gpar(fontsize=geneLab, fontface="bold"),
                    row_names_side="left",
                    row_names_max_width=unit(15, "cm"),
                    row_dend_width=unit(10,"mm"),

                    cluster_columns=T,
                    show_column_dend=T,
                    column_title="Enriched terms",
                    column_title_side="top",
                    column_title_gp=gpar(fontsize=12, fontface="bold"),
                    column_title_rot=0,
                    show_column_names=FALSE,
                    #column_names_gp=gpar(fontsize=termLab, fontface="bold"),
                    #column_names_max_height=unit(15, "cm"),

                    show_heatmap_legend=FALSE,

                    #width=unit(12.5, "cm"),

                    clustering_distance_columns="euclidean",
                    clustering_method_columns="ward.D2",
                    clustering_distance_rows="euclidean",
                    clustering_method_rows="ward.D2",

                    bottom_annotation=haTerms)

draw(hmapGSEA + haGenes, heatmap_legend_side="right", annotation_legend_side="right")
dev.off()
</code></pre>

<p>However there is an error message after annGSEA: </p>

<pre><code>dput(annGSEA)
structure(list(), .Names = character(0), row.names = "c(\"LRP1\", \"ELAVL4\", \"ENOX1\", \"TRIP6\", \"KHDRBS3\", \"TDRD9\", \"THOC6\", \"CPSF1\", \"HSPB1\", \"SF3A2\", \"STXBP1\", \"DUS3L\", \"INTS1\", \"DZIP1L\", \"HIST1H1B\", \"TRMT2A\", \"RPUSD1\", \"MRPS2\", \"EXOSC5\", \"TDRD1\", \"PURG\", \"NOL12\", \"TRMT61A\", \"XAB2\", \"TRMT1\", \"PTRF\", \"POLR2I\", \"MAZ\", \"TBL3\", \"BOP1\", \"RBM10\", \"TSR3\", \"SART1\", \"CCDC86\", \"SAMD4A\", \"RBM11\", \"RPS5\", \"HNRNPLL\", \"POLRMT\", \"NSUN7\", \"PABPC5\", \"DDX54\", \"PRRC2B\", \"RPS15\", \"MYBBP1A\", \"DUS1L\", \"ARHGEF28\", \"RPL28\", \"ZNF598\", \"ZMAT5\", \"RPL36\", \"RPL8\", \"DHX37\", \"ZC3H7B\", \n\"RRP9\", \"PQBP1\", \"ZNF385A\", \"PUS1\", \"DDX49\", \"TCOF1\", \"BICC1\", \"GLTSCR2\", \"SCAF1\", \"MRPL4\", \"FSCN1\", \"EDF1\", \"NOVA1\", \"PCBP3\", \"FBL\", \"MRPL55\", \"PUF60\", \"NYNRIN\", \"ZFP36L1\", \"RPS9\", \"MKRN3\", \"GTF2F1\", \"EEFSEC\", \"FARSA\", \"TARBP2\", \"RPL35\", \"RPS19\", \"ZC3H3\", \"H1F0\", \"BST2\", \"FASN\", \"ZYX\", \"NOC4L\", \"LONP1\", \"RUVBL2\", \"MRPL38\", \"TRAP1\", \"TUFM\", \"RBM42\", \"TNS1\", \"EDC4\", \"WDR6\", \"PCBP4\", \"PUSL1\", \"EEF2\", \"RPS28\", \"RAVER1\", \"APEH\", \"TSEN54\", \"VARS\", \"C7orf50\", \"GRN\", \"ARHGEF1\", \"SF3B5\", \"RPL18\", \"EIF3G\", \n\"ANG\", \"EIF5AL1\", \"HIST1H1C\", \"RPL13\", \"U2AF1L4\", \"C9orf114\", \"FASTK\", \"TSEN34\", \"SRRT\", \"RPS2\", \"MRPL54\", \"CSRP1\", \"HELZ2\", \"RPLP2\", \"RPL18A\", \"PRRC2A\", \"GTPBP1\", \"NOC2L\", \"RBM19\", \"RNASEH2A\", \"ADARB2\", \"SERPINH1\", \"CCDC9\", \"DXO\", \"GNB2L1\", \"FLNA\", \"RNASEH2C\", \"IPO13\", \"HABP4\", \"C11orf68\", \"QTRT1\", \"DGCR14\", \"RPL3\", \"SETD1A\", \"GEMIN4\", \"NPM2\", \"MRPS26\", \"RRP7A\", \"CCDC124\", \"CACTIN\", \"ISG20\", \"INTS5\", \"SNTB2\", \"RPUSD3\", \"RPL29\", \"PPRC1\", \"PPAN\", \"PRPF40B\", \"RBFOX2\", \"C15orf52\", \"ALYREF\", \"EXOSC4\", \n\"GNL1\", \"SIDT2\", \"REPIN1\", \"CHERP\", \"NOB1\", \"RPLP1\", \"EIF5A2\", \"RRP1\", \"MRPL41\", \"RPL19\", \"SUGP1\", \"NAA38\", \"CDC42EP4\", \"EEF1D\", \"DDX41\", \"PRPF19\", \"CLASRP\", \"PRPF6\", \"ZC3H12B\", \"SNRPB\", \"MEPCE\", \"COL14A1\", \"WBSCR16\", \"LSM7\", \"PELP1\", \"VARS2\", \"TRPT1\", \"RPS10\", \"PTBP1\", \"RPS8\", \"CPSF3L\", \"NOSIP\", \"TCF20\", \"PTCD1\", \"APEX1\", \"C1orf35\", \"MRPL23\", \"TWF2\", \"CTIF\", \"DHX38\", \"MRPS34\", \"SYMPK\", \"U2AF2\", \"QARS\", \"CCAR2\", \"RPS3\", \"RPS16\", \"P4HB\", \"MVP\", \"POLR2J\", \"SKIV2L\", \"GTPBP3\", \"ZNF768\", \"UBA52\", \"SUPT5H\", \n\"POLR2L\", \"POLR2A\", \"EIF3K\", \"R3HCC1\", \"PIH1D1\", \"ATXN2L\", \"OAS3\", \"IPO4\", \"CCDC137\", \"SETD1B\", \"ILF3\", \"TBRG4\", \"PKM\", \"AARS2\", \"FAU\", \"ACTN4\", \"RPS19BP1\", \"ANGEL1\", \"PLD6\", \"MOV10\", \"EIF6\", \"DRG2\", \"AARS\", \"PRR3\", \"AC004381.6\", \"RBPMS\", \"CPSF4\", \"NOL6\", \"RPL13A\", \"NPM3\", \"UBA1\", \"REXO4\", \"RRP12\", \"UPF1\", \"RPL11\", \"DDX43\", \"SNRPA\", \"ISY1\", \"MRPS18A\", \"RBMS1\", \"CSTB\", \"FKBP3\", \"MTIF3\", \"MRPL39\", \"CLK4\", \"SRP54\", \"ERI1\", \"CLK1\", \"IMP3\", \"GRSF1\", \"GTF3A\", \"FASTKD1\", \"DYNC1LI1\", \"PTGES3\", \"TRIT1\", \"EXOSC3\", \n\"IGF2BP3\", \"TRIM71\", \"MCTS1\", \"GEMIN2\", \"SUMO1\", \"NQO1\", \"HSPA8\", \"POLR2G\", \"TAF9\", \"MRPL33\", \"FAM46A\", \"MRPS36\", \"FNDC3B\", \"DDX52\", \"DYNLL1\", \"RBM43\", \"MANF\", \"TDRD7\", \"AHNAK\", \"IFIT2\", \"ZMAT3\", \"APOBEC3H\", \"RTN4\", \"S100A4\", \"PIH1D2\", \"ANXA2\", \"PIWIL3\", \"TMSB4X\", \"PIWIL4\", \"RNASE6\", \"LGALS1\", \"RNASE3\", \"TLR7\", \"MAEL\", \"SAMHD1\", \"RNASE2\", \"C2orf15\", \"SIDT1\", \"HERC5\", \"PSIP1\", \"RPL17\", \"ZC3H12C\", \"SLC16A3\", \"TEP1\", \"HEXIM1\", \"CPEB4\", \"ZC3H12D\", \"CORO1A\", \"ZFP36\", \"KIF1C\", \"WARS\", \"CCRN4L\", \"AFF2\", \n\"TST\", \"RBM47\", \"LGALS3\", \"NXF3\", \"PPARGC1A\", \"TLR8\")", class = "data.frame")
&gt; 
</code></pre>

CC BY-SA 4.0
2018-10-31T09:53:33.380Z
I think you forgot the link to the paper you are referencing. You tagged the question with [tag:R], which problem have with which code? Perhaps you want to make the figure B and you don't know how?
llrs
CC BY-SA 4.0
2018-10-31T10:20:40.763Z
yes i m trying to make figure and truly i don;t know how to begin with
kcm
CC BY-SA 4.0
2018-10-31T10:31:03.403Z
You added a lot of code, you already seem how to start! What is the output of this code? (could you upload the hmapGSEA plot?) What didn't you like or is not working as expected?
llrs
CC BY-SA 4.0
2018-10-31T13:13:22.470Z
I took this code from biostar, im stuck at the annGSEA after that when i loop through it doesn't match the pattern of genes would give the error message in the question have a look
kcm
CC BY-SA 4.0
2018-10-31T18:27:40.150Z
Please provide the output for the variable `pattern`, the error points to there being something wrong with that. Also, it looks like you didn't copy paste the error message correctly. Give us the full message and it'll be easier the pin the issue down.
Kohl Kinning
CC BY-SA 4.0
2018-11-01T05:22:36.847Z
i should use dput to make it clear perhaps.
kcm
<r><rna-seq><visualization><figure-reproduction><heatmap>
GO Term heatmap plot in terms of P value or fold enrichment
# GO Term heatmap plot in terms of P value or fold enrichment

(Asked by: username_0 on 2018-10-31)

I'm clustering genes in terms of expression after clustering them. I'm taking out clusters and trying to find out what kind of GO terms are coming up. I came across this figure from this paper, I want to do as the figure B:
Here you can find the file I intend to use to make something like the above plot. 
I am using this the code from a question in Biostar:
DAVIDfile <- "DAVID.txt"
DAVID <- read.table(DAVIDfile, sep="\t", header=TRUE)
colnames(DAVID)
class(DAVID)

enrichBcutoff <- 0.05
DAVID <- subset(DAVID, Benjamini< enrichBcutoff)
DAVID <- DAVID[,c(1,2,3,5,6,10)]

head(DAVID)

A <- data.frame(sigGeneList)

annGSEA <- data.frame(row.names=A)
for (j in 1:length(sigGeneList))
{
  gene <- sigGeneList[j]
  pattern <- paste("^", gene, ", |, ", gene, "$| ", gene, ",", sep="")
    for (k in 1:nrow(DAVID))
  {
    if (any(grepl(pattern, DAVID$Genes[k])))
    {
      annGSEA[j,k] <- 1
    }
    else
    {
      annGSEA[j,k] <- 0
    }
  }
}
colnames(annGSEA) <- DAVID[,2]

annGSEA <- annGSEA[,apply(annGSEA, 2, mean)!=0]

annGSEA <- annGSEA[apply(annGSEA, 1, mean)!=0,]


require(ComplexHeatmap)
require(circlize)

topTable <- topTable[which(topTable$Gene %in% rownames(annGSEA)),]
topTable <- topTable[match(rownames(annGSEA), topTable$Gene),]

geneLab=10
termLab=8

#Create heatmap annotations
dfMinusLog10FDRGenes <- data.frame(-log10(topTable[which(topTable[,1] %in% rownames(annGSEA)),"padj"]))
dfMinusLog10FDRGenes[dfMinusLog10FDRGenes=="Inf"] <- 0
dfFoldChangeGenes <- data.frame(topTable[which(topTable[,1] %in% rownames(annGSEA)),"log2FoldChange"])
dfGeneAnno <- data.frame(dfMinusLog10FDRGenes, dfFoldChangeGenes)
colnames(dfGeneAnno) <- c("DEG\nsignificance\nscore", "Regulation")
dfGeneAnno[,2] <- ifelse(dfGeneAnno[,2]>0, "Up-regulated", "Down-regulated")
colours <- list("Regulation"=c("Up-regulated"="royalblue", "Down-regulated"="yellow"))
haGenes <- rowAnnotation(df=dfGeneAnno, col=colours, width=unit(1,"cm"))

dfMinusLog10BenjaminiTerms <- data.frame(-log10(read.table(DAVIDfile, sep="\t", header=TRUE)[which(read.table(DAVIDfile, sep="\t", header=TRUE)$Term %in% colnames(annGSEA)),"Benjamini"]))
colnames(dfMinusLog10BenjaminiTerms) <- "GO Term\nsignificance\nscore"
haTerms <- HeatmapAnnotation(df=dfMinusLog10BenjaminiTerms,
                             colname=anno_text(colnames(annGSEA), rot=40, just="right", offset=unit(1,"npc")-unit(2,"mm"), gp=gpar(fontsize=termLab)),
                             annotation_height=unit.c(unit(1, "cm"), unit(8, "cm")))

pdf("GO.pdf", width=7, height=12)
hmapGSEA <- Heatmap(annGSEA,

                    name="My enrichment",

                    split=dfGeneAnno[,2],

                    col=c("0"="white", "1"="forestgreen"),

                    rect_gp=gpar(col="grey85"),

                    cluster_rows=T,
                    show_row_dend=T,
                    row_title="Statistically-significant genes",
                    row_title_side="left",
                    row_title_gp=gpar(fontsize=12, fontface="bold"),
                    row_title_rot=0,
                    show_row_names=TRUE,
                    row_names_gp=gpar(fontsize=geneLab, fontface="bold"),
                    row_names_side="left",
                    row_names_max_width=unit(15, "cm"),
                    row_dend_width=unit(10,"mm"),

                    cluster_columns=T,
                    show_column_dend=T,
                    column_title="Enriched terms",
                    column_title_side="top",
                    column_title_gp=gpar(fontsize=12, fontface="bold"),
                    column_title_rot=0,
                    show_column_names=FALSE,
                    #column_names_gp=gpar(fontsize=termLab, fontface="bold"),
                    #column_names_max_height=unit(15, "cm"),

                    show_heatmap_legend=FALSE,

                    #width=unit(12.5, "cm"),

                    clustering_distance_columns="euclidean",
                    clustering_method_columns="ward.D2",
                    clustering_distance_rows="euclidean",
                    clustering_method_rows="ward.D2",

                    bottom_annotation=haTerms)

draw(hmapGSEA + haGenes, heatmap_legend_side="right", annotation_legend_side="right")
dev.off()

However there is an error message after annGSEA: 
dput(annGSEA)
structure(list(), .Names = character(0), row.names = "c(\"LRP1\", \"ELAVL4\", \"ENOX1\", \"TRIP6\", \"KHDRBS3\", \"TDRD9\", \"THOC6\", \"CPSF1\", \"HSPB1\", \"SF3A2\", \"STXBP1\", \"DUS3L\", \"INTS1\", \"DZIP1L\", \"HIST1H1B\", \"TRMT2A\", \"RPUSD1\", \"MRPS2\", \"EXOSC5\", \"TDRD1\", \"PURG\", \"NOL12\", \"TRMT61A\", \"XAB2\", \"TRMT1\", \"PTRF\", \"POLR2I\", \"MAZ\", \"TBL3\", \"BOP1\", \"RBM10\", \"TSR3\", \"SART1\", \"CCDC86\", \"SAMD4A\", \"RBM11\", \"RPS5\", \"HNRNPLL\", \"POLRMT\", \"NSUN7\", \"PABPC5\", \"DDX54\", \"PRRC2B\", \"RPS15\", \"MYBBP1A\", \"DUS1L\", \"ARHGEF28\", \"RPL28\", \"ZNF598\", \"ZMAT5\", \"RPL36\", \"RPL8\", \"DHX37\", \"ZC3H7B\", \n\"RRP9\", \"PQBP1\", \"ZNF385A\", \"PUS1\", \"DDX49\", \"TCOF1\", \"BICC1\", \"GLTSCR2\", \"SCAF1\", \"MRPL4\", \"FSCN1\", \"EDF1\", \"NOVA1\", \"PCBP3\", \"FBL\", \"MRPL55\", \"PUF60\", \"NYNRIN\", \"ZFP36L1\", \"RPS9\", \"MKRN3\", \"GTF2F1\", \"EEFSEC\", \"FARSA\", \"TARBP2\", \"RPL35\", \"RPS19\", \"ZC3H3\", \"H1F0\", \"BST2\", \"FASN\", \"ZYX\", \"NOC4L\", \"LONP1\", \"RUVBL2\", \"MRPL38\", \"TRAP1\", \"TUFM\", \"RBM42\", \"TNS1\", \"EDC4\", \"WDR6\", \"PCBP4\", \"PUSL1\", \"EEF2\", \"RPS28\", \"RAVER1\", \"APEH\", \"TSEN54\", \"VARS\", \"C7orf50\", \"GRN\", \"ARHGEF1\", \"SF3B5\", \"RPL18\", \"EIF3G\", \n\"ANG\", \"EIF5AL1\", \"HIST1H1C\", \"RPL13\", \"U2AF1L4\", \"C9orf114\", \"FASTK\", \"TSEN34\", \"SRRT\", \"RPS2\", \"MRPL54\", \"CSRP1\", \"HELZ2\", \"RPLP2\", \"RPL18A\", \"PRRC2A\", \"GTPBP1\", \"NOC2L\", \"RBM19\", \"RNASEH2A\", \"ADARB2\", \"SERPINH1\", \"CCDC9\", \"DXO\", \"GNB2L1\", \"FLNA\", \"RNASEH2C\", \"IPO13\", \"HABP4\", \"C11orf68\", \"QTRT1\", \"DGCR14\", \"RPL3\", \"SETD1A\", \"GEMIN4\", \"NPM2\", \"MRPS26\", \"RRP7A\", \"CCDC124\", \"CACTIN\", \"ISG20\", \"INTS5\", \"SNTB2\", \"RPUSD3\", \"RPL29\", \"PPRC1\", \"PPAN\", \"PRPF40B\", \"RBFOX2\", \"C15orf52\", \"ALYREF\", \"EXOSC4\", \n\"GNL1\", \"SIDT2\", \"REPIN1\", \"CHERP\", \"NOB1\", \"RPLP1\", \"EIF5A2\", \"RRP1\", \"MRPL41\", \"RPL19\", \"SUGP1\", \"NAA38\", \"CDC42EP4\", \"EEF1D\", \"DDX41\", \"PRPF19\", \"CLASRP\", \"PRPF6\", \"ZC3H12B\", \"SNRPB\", \"MEPCE\", \"COL14A1\", \"WBSCR16\", \"LSM7\", \"PELP1\", \"VARS2\", \"TRPT1\", \"RPS10\", \"PTBP1\", \"RPS8\", \"CPSF3L\", \"NOSIP\", \"TCF20\", \"PTCD1\", \"APEX1\", \"C1orf35\", \"MRPL23\", \"TWF2\", \"CTIF\", \"DHX38\", \"MRPS34\", \"SYMPK\", \"U2AF2\", \"QARS\", \"CCAR2\", \"RPS3\", \"RPS16\", \"P4HB\", \"MVP\", \"POLR2J\", \"SKIV2L\", \"GTPBP3\", \"ZNF768\", \"UBA52\", \"SUPT5H\", \n\"POLR2L\", \"POLR2A\", \"EIF3K\", \"R3HCC1\", \"PIH1D1\", \"ATXN2L\", \"OAS3\", \"IPO4\", \"CCDC137\", \"SETD1B\", \"ILF3\", \"TBRG4\", \"PKM\", \"AARS2\", \"FAU\", \"ACTN4\", \"RPS19BP1\", \"ANGEL1\", \"PLD6\", \"MOV10\", \"EIF6\", \"DRG2\", \"AARS\", \"PRR3\", \"AC004381.6\", \"RBPMS\", \"CPSF4\", \"NOL6\", \"RPL13A\", \"NPM3\", \"UBA1\", \"REXO4\", \"RRP12\", \"UPF1\", \"RPL11\", \"DDX43\", \"SNRPA\", \"ISY1\", \"MRPS18A\", \"RBMS1\", \"CSTB\", \"FKBP3\", \"MTIF3\", \"MRPL39\", \"CLK4\", \"SRP54\", \"ERI1\", \"CLK1\", \"IMP3\", \"GRSF1\", \"GTF3A\", \"FASTKD1\", \"DYNC1LI1\", \"PTGES3\", \"TRIT1\", \"EXOSC3\", \n\"IGF2BP3\", \"TRIM71\", \"MCTS1\", \"GEMIN2\", \"SUMO1\", \"NQO1\", \"HSPA8\", \"POLR2G\", \"TAF9\", \"MRPL33\", \"FAM46A\", \"MRPS36\", \"FNDC3B\", \"DDX52\", \"DYNLL1\", \"RBM43\", \"MANF\", \"TDRD7\", \"AHNAK\", \"IFIT2\", \"ZMAT3\", \"APOBEC3H\", \"RTN4\", \"S100A4\", \"PIH1D2\", \"ANXA2\", \"PIWIL3\", \"TMSB4X\", \"PIWIL4\", \"RNASE6\", \"LGALS1\", \"RNASE3\", \"TLR7\", \"MAEL\", \"SAMHD1\", \"RNASE2\", \"C2orf15\", \"SIDT1\", \"HERC5\", \"PSIP1\", \"RPL17\", \"ZC3H12C\", \"SLC16A3\", \"TEP1\", \"HEXIM1\", \"CPEB4\", \"ZC3H12D\", \"CORO1A\", \"ZFP36\", \"KIF1C\", \"WARS\", \"CCRN4L\", \"AFF2\", \n\"TST\", \"RBM47\", \"LGALS3\", \"NXF3\", \"PPARGC1A\", \"TLR8\")", class = "data.frame")
>

**Tags:** r, rna-seq, visualization, figure-reproduction, heatmap
> **Comments:**
> **username_1**: I think you forgot the link to the paper you are referencing. You tagged the question with [tag:R], which problem have with which code? Perhaps you want to make the figure B and you don't know how?  
> **username_0**: yes i m trying to make figure and truly i don;t know how to begin with  
> **username_1**: You added a lot of code, you already seem how to start! What is the output of this code? (could you upload the hmapGSEA plot?) What didn't you like or is not working as expected?  
> **username_0**: I took this code from biostar, im stuck at the annGSEA after that when i loop through it doesn't match the pattern of genes would give the error message in the question have a look  
> **username_2**: Please provide the output for the variable `pattern`, the error points to there being something wrong with that. Also, it looks like you didn't copy paste the error message correctly. Give us the full message and it'll be easier the pin the issue down.  
> **username_0**: i should use dput to make it clear perhaps.  

---

## 0 answers

