# HG changeset patch
# User artbio
# Date 1561398008 14400
# Node ID baf7a079bce04f4be166e552c4918a647cc87540

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe

diff -r 000000000000 -r baf7a079bce0 signature_score.R
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/signature_score.R	Mon Jun 24 13:40:08 2019 -0400
@@ -0,0 +1,230 @@
+#########################
+#    Signature score    #
+#########################
+
+# Compute the signature score based on the geometric mean of the target gene expression
+# and split cells  in 2 groups (high/low) using this signature score.
+
+# Example of command
+# Rscript 4-signature_score.R --input <input.tsv> --genes  ARNT2,SALL2,SOX9,OLIG2,POU3F2
+#                             --output <output.tab> --pdf <output.pdf>
+
+# load packages that are provided in the conda env
+options( show.error.messages=F,
+       error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
+loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
+warnings()
+
+library(optparse)
+library(psych)
+library(ggplot2)
+library(gridExtra)
+
+# Arguments
+option_list = list(
+  make_option(
+    "--input",
+    default = NA,
+    type = 'character',
+    help = "Input file that contains log2(CPM +1) values"
+  ),
+  make_option(
+    "--sep",
+    default = '\t',
+    type = 'character',
+    help = "File separator [default : '%default' ]"
+  ),
+  make_option(
+    "--colnames",
+    default = TRUE,
+    type = 'logical',
+    help = "Consider first line as header ? [default : '%default' ]"
+  ),  
+  make_option(
+    "--genes",
+    default = NA,
+    type = 'character',
+    help = "List of genes comma separated"
+  ),
+  make_option(
+    "--percentile_threshold",
+    default = 20,
+    type = 'integer',
+    help = "detection threshold to keep a gene in signature set [default : '%default' ]"
+  ),
+  make_option(
+    "--output",
+    default = "./output.tab",
+    type = 'character',
+    help = "Output path [default : '%default' ]"
+  ),
+  make_option(
+    "--stats",
+    default = "./statistics.tab",
+    type = 'character',
+    help = "statistics path [default : '%default' ]"
+  ),
+  make_option(
+    "--pdf",
+    default = "~/output.pdf",
+    type = 'character',
+    help = "pdf path [default : '%default' ]"
+  )
+)
+
+opt = parse_args(OptionParser(option_list = option_list),
+                 args = commandArgs(trailingOnly = TRUE))
+
+if (opt$sep == "tab") {opt$sep = "\t"}
+if (opt$sep == "comma") {opt$sep = ","}
+
+# Take input data
+data.counts <- read.table(
+  opt$input,
+  h = opt$colnames,
+  row.names = 1,
+  sep = opt$sep,
+  check.names = F
+)
+
+# Get vector of target genes
+genes <- unlist(strsplit(opt$genes, ","))
+
+if (length(unique(genes %in% rownames(data.counts))) == 1) {
+  if (unique(genes %in% rownames(data.counts)) == F)
+    stop("None of these genes are in your dataset: ", opt$genes)
+}
+    
+logical_genes <- rownames(data.counts) %in% genes
+
+# Retrieve target genes in counts data
+signature.counts <- subset(data.counts, logical_genes)
+
+
+## Descriptive Statistics Function
+descriptive_stats = function(InputData) {
+  SummaryData = data.frame(
+    mean = rowMeans(InputData),
+    SD = apply(InputData, 1, sd),
+    Variance = apply(InputData, 1, var),
+    Percentage_Detection = apply(InputData, 1, function(x, y = InputData) {
+      (sum(x != 0) / ncol(y)) * 100
+    })
+  )
+  return(SummaryData)
+}
+
+signature_stats <- descriptive_stats(signature.counts)
+
+# Find poorly detected genes from the signature 
+kept_genes <- signature_stats$Percentage_Detection >= opt$percentile_threshold
+
+# Add warnings
+if (length(unique(kept_genes)) > 1) {
+  cat(
+    "WARNINGS ! Following genes were removed from further analysis due to low gene expression :",
+    paste(paste(rownames(signature.counts)[!kept_genes], round(signature_stats$Percentage_Detection[!kept_genes], 2), sep = " : "), collapse = ", "),
+    "\n"
+  )
+} else {
+  if (unique(kept_genes) == F) {
+    stop(
+      "None of these genes are detected in ",
+      opt$percent,
+      "% of your cells: ",
+      paste(rownames(signature_stats), collapse = ", "),
+      ". You can be less stringent thanks to --percent parameter."
+    )
+  }
+}
+
+# Remove genes poorly detected in the dataset
+signature.counts <- signature.counts[kept_genes,]
+    
+# Replace 0 by 1 counts
+signature.counts[signature.counts == 0] <- 1
+
+# Geometric mean by cell
+score <- apply(signature.counts, 2, geometric.mean) # geometric.mean requires psych
+
+# Add results in signature_output
+signature_output <- data.frame(
+                         cell = names(score),
+                         score = score,
+                         rate = ifelse(score > mean(score), "HIGH", "LOW"),
+                         nGenes = colSums(data.counts != 0),
+                         total_counts = colSums(data.counts)
+                         )
+
+# statistics of input genes, signature genes first lines
+statistics.counts <- rbind(subset(data.counts, logical_genes),
+                    subset(data.counts, !logical_genes))  
+statistics <- descriptive_stats(statistics.counts)
+statistics <- cbind(gene=rownames(statistics), statistics)
+
+
+
+# Re-arrange score matrix for plots
+score <- data.frame(score = score,
+                    order = rank(score, ties.method = "first"),
+                    signature = signature_output$rate,
+                    stringsAsFactors = F)
+
+pdf(file = opt$pdf)
+
+ggplot(score, aes(x = order, y = score)) +
+  geom_line() + 
+  geom_segment(x = 0, xend = max(score$order[score$signature == "LOW"]), y = mean(score$score), yend = mean(score$score)) +
+  geom_area(aes(fill = signature), alpha = .7) +
+  scale_fill_manual(values=c("#ff0000", "#08661e")) +
+  geom_text(aes(x = 1, y = mean(score)), label = "Mean", vjust = -0.3, colour = "black") +
+  labs(title = "Ordered cell signature scores", x = "Cell index", y = "Score")
+
+density_score <- density(score$score)
+ggplot(data.frame(density_score[1:2]), aes(x, y, fill = ifelse(x < mean(score$score), "LOW", "HIGH"))) +
+  geom_line() +
+  geom_vline(xintercept = mean(score$score)) +
+  geom_text(x = mean(score$score), y = max(density_score$y), label = "Mean", hjust = -0.3, colour = "black") +
+  geom_area(alpha = .7) +
+  scale_fill_manual(values=c("#ff0000", "#08661e")) +
+  ylim(0, max(density_score$y)) +
+  labs(
+    title = "Distribution of Cell signature scores",
+    x = paste("N =", density_score$n, "Bandwidth =", density_score$bw),
+    y = "Density",
+    fill = "Signature"
+  )
+
+# Check score independant of low expression
+p_gene <- ggplot(signature_output, aes(rate, nGenes)) +
+  geom_violin(aes(fill = rate), alpha = .5, trim = F, show.legend = F) +
+  scale_fill_manual(values=c("#ff0000", "#08661e")) +
+  geom_jitter() + labs(y = "Number of detected genes", x = "Signature")
+
+p_counts <- ggplot(signature_output, aes(rate, total_counts)) +
+  geom_violin(aes(fill = rate), alpha = .5, trim = F, show.legend = F) +
+  scale_fill_manual(values=c("#ff0000", "#08661e")) +
+  geom_jitter() + labs(y = "Total counts", x = "Signature")
+
+grid.arrange(p_gene, p_counts, ncol = 2, top = "Influence of library sequencing depth on cell signature scores")
+
+dev.off()
+
+# Save file
+write.table(
+  signature_output,
+  opt$output,
+  sep = "\t",
+  quote = F,
+  col.names = T,
+  row.names = F
+)
+
+write.table(
+  statistics,
+  opt$stats,
+  sep = "\t",
+  quote = F,
+  col.names = T,
+  row.names = F
+)
\ No newline at end of file
diff -r 000000000000 -r baf7a079bce0 signature_score.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/signature_score.xml	Mon Jun 24 13:40:08 2019 -0400
@@ -0,0 +1,98 @@
+<tool id="signature_score" name="Compute signature scores" version="0.9.0">
+    <description>in single cell RNAseq</description>
+    <requirements>
+        <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement>
+        <requirement type="package" version="2.2.1=r3.3.2_0">r-ggplot2</requirement>
+        <requirement type="package" version="2.3=r3.3.2_0">r-gridextra</requirement>
+        <requirement type="package" version="1.6.9=r3.3.2_0">r-psych</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" level="fatal" description="Tool exception" />
+    </stdio>
+    <command detect_errors="exit_code"><![CDATA[ 
+        Rscript $__tool_directory__/signature_score.R 
+            --input $input 
+            --sep 
+            #if $sep == 'tab':
+              'tab'
+            #elif $sep == 'comma':
+              'comma'
+            #end if
+            --genes '$genes'
+            --percentile_threshold '$threshold'
+            --output '$output'
+            --stats '$stats'
+            --pdf '$pdf'
+]]></command>
+    <inputs>
+        <param name="input" type="data" format="txt,tabular" label="Raw counts of expression data"/>
+        <param name="sep" type="select" label="Indicate column separator">
+            <option value="tab" selected="true">Tabs</option>
+            <option value="comma">Comma</option>
+        </param>
+        <param name="genes" type="text" value="" label="Comma-separated list of genes to include in signature"
+               help="Comma-separated list of genes to include in signature, eg &quot;ZNF454,GAPDH,LAIR1,ACAD9,CHTOP&quot;" />
+        <param name="threshold" type="float" value="20.0" label="Threshold to keep a proposed gene in the effective signature"
+               help="signature gene that are not expressed in at least this percentage of cells will not be kept to compute the effective signature" />
+    </inputs>
+    <outputs>
+        <data name="pdf" format="pdf" label="Plots from ${on_string}" />
+        <data name="output" format="tabular" label="signature scores from ${on_string}" />
+        <data name="stats" format="tabular" label="genes statistics in ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="gene_filtered_input.tsv" ftype="txt"/>
+            <param name="sep" value='tab' />
+            <param name="genes" value="ZNF454,GAPDH,LAIR1,ACAD9,CHTOP" />
+            <output name="pdf" file="signature.pdf" ftype="pdf" compare="sim_size" delta="200" />
+            <output name="output" file="signature.tsv" ftype="tabular"/>
+            <output name="stats" file="gene_stats.tsv" ftype="tabular"/>
+        </test>
+    </tests>
+    <help>
+
+**What it does**
+
+The tools takes a table of _normalized_ gene expression values (rows) in single cell RNAseq library sequencing (columns)
+and a comma-separated list of genes, and returns in a table the geometric mean of expression of these
+genes for each cell/library. This geometric mean is considered as the score for the genes signature for a given cell/library. 
+
+
+**Inputs**
+
+A table of comma (csv) or tabulation (tsv) separated values.
+Gene names should be in the first column and cell names should be in the first row.
+Note that in a number of a csv files, header of the gene column is omitted, resulting in
+a first row with one item less than in other rows. This is handled by the tool that
+recognises this situation.
+
+A comma separated list of genes desired as contributing to the signature score of the cell/library
+
+The expression threshold for signature genes (the aforementioned gene list) to be effectively
+taken into account to compute signature scores. By default, genes are taken into account if
+they are expressed in at least 20% of cells/libraries
+
+** Outputs **
+The tools returns a table "signature scores" that contains
+
+* the cell/library identifier
+* the signature score for this identifier
+* the rate of the signature score, ie whether it is higher (HIGH) or lower (LOW) that the average signature score in all cells/libraries
+* the number of genes detected in the cell/library
+* the total number of aligned reads in the cell/library
+
+    </help>
+    <citations>
+        <citation type="bibtex">
+        @Manual{,
+             title = {R: A Language and Environment for Statistical Computing},
+             author = {{R Core Team}},
+             organization = {R Foundation for Statistical Computing},
+             address = {Vienna, Austria},
+             year = {2014},
+             url = {http://www.R-project.org/},
+        }
+        </citation>
+    </citations>
+</tool>
diff -r 000000000000 -r baf7a079bce0 test-data/gene_filtered_input.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gene_filtered_input.tsv	Mon Jun 24 13:40:08 2019 -0400
@@ -0,0 +1,43 @@
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+CCT4	0	12.5608159031083	0	11.6111039620927	0	0	14.928561508656	0	0	0	0	14.52014278721	0	0	11.5947317819049	13.5265493694117	0	14.5523673454284	0	0	0	15.9852625308647	0	16.4105528076041	0	0	0	0	16.2446864845683	16.2547020303542	0	0	15.8593701506428	15.1207620425777	9.20016066961385	0	0	0	14.4878984272626	0	0	0	15.541044014531	10.3857528419314	0	0	0	17.0657644331678	0	0	0	0	0	14.3233193729971	17.5959263690384	11.9448736109475	11.8757664188696	0	14.6822904799705	0	0	12.9902091512766	0	0	8.64976283074145	14.5429704635478	14.3226185868992	0	11.0413810146209	0	0	0	0	0	0	18.0463061150311	0	0	18.2955113945436	13.7899945334298	0	0	0	0	9.4501526353054	14.1458493811894	0	0	14.3241281556631	15.8744665433559	0	14.9429296873924	0	9.8996567204838	0	0	15.2083870890718	13.5091924972372	0	13.6854773101127
+OBFC2B	0	14.7782198861919	0	0	0	0	0	0	0	0	0	0	0	0	13.1090017252155	13.2204751387523	0	0	0	0	0	0	0	0	0	0	0	15.8311914189231	0	0	0	0	13.2009554691452	13.3838909271687	0	0	0	15.1397944602615	13.7044355367675	0	0	0	0	15.7597395438236	0	0	9.83478813017416	0	0	0	0	0	0	9.61543117273472	0	0	13.2381018765857	0	0	0	0	0	0	0	0	0	0	15.3379168100524	0	16.3502711141373	0	0	0	0	0	0	0	0	0	12.1672760205714	0	0	10.8389388619384	0	12.745979233988	0	0	0	14.2519819769156	0	0	0	0	0	0	0	0	0	0	13.7496028864221
+APIP	0	0	0	0	0	0	14.5053658491751	0	0	0	0	0	0	0	0	0	0	11.1508435020056	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9.58377370079595	0	0	0	0	0	0	0	0	0	0	0	18.0252207984696	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17.3115111369962	0	0	0	0	0	0	0	0	0	0	16.5814087488351	0	7.79057632864985	15.4795417723719	8.52702242192133	18.059448673161	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11.5584567691369	0	0
+CHTOP	16.745054735021	0	17.3466147247473	0	15.7799131839274	15.8122374661064	9.63265326937863	0	0	13.4512041535885	14.520118984713	0	0	0	0	12.4392240619043	0	0	9.5452144270117	14.938904538072	10.825146920729	0	13.2340556798273	11.318344169959	0	0	0	15.8822647427747	16.7374499112429	0	0	0	13.5295470065472	0	9.46278622874624	0	7.98091432025088	0	11.2336209877566	0	0	13.6786296929006	17.4104379269865	14.4722004278722	0	0	0	0	0	0	17.0198066091866	8.46474483194135	13.9009957461827	10.7299176833861	0	0	13.5706464736428	0	0	0	0	0	0	0	0	0	13.2378086321315	0	0	0	18.1641616693075	0	13.4398453097056	0	0	0	0	0	0	10.1093752472331	0	0	0	14.019026433977	12.745979233988	0	0	0	0	0	0	16.5591574545572	0	10.3143165799555	0	0	0	13.9273047730215	0	13.0334631866655
+CHFR	0	10.9424005948458	13.7358474563822	12.7386093483035	0	0	0	0	0	0	10.5210397222539	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	18.5145545583833	0	0	0	0	0	17.4405491237334	10.2982667055414	0	0	13.0454659231443	0	11.0547071854939	16.8254795670235	14.0851968356427	0	0	0	0	0	14.2438696254744	0	0	0	0	0	0	0	0	0	14.5917769944055	0	0	18.5411128749616	0	0	12.4291553814253	0	0	0	0	0	0	0	18.4629341793756	0	0	0	13.8065141346015	0	12.1083954006359	0	0	0	11.9551725747085	14.7211605644646	0	0	14.1615733911273	9.96794706612638	0	0	0	0	9.8996567204838	13.8415544299119	0	0	0	0	0
+PSPH	0	11.3827802431641	0	13.3950479346999	0	0	9.63265326937863	13.8775309918482	0	0	0	0	0	0	0	13.9468502676446	0	0	11.8655969070345	0	0	0	0	13.4053749225104	0	0	15.5161365961368	0	0	0	0	0	15.8325539409012	0	0	0	9.97662501806838	0	12.4742833966341	0	0	14.9609646288519	0	0	0	0	7.83951982992838	0	0	0	0	0	0	14.6940185938879	0	0	11.768880745047	16.7642583238722	0	0	0	0	0	0	0	0	11.7172556561314	0	12.1785111141961	0	0	0	0	0	0	0	11.7760775533159	12.8717009683037	0	14.9282938714688	0	0	12.8383480095263	0	14.2382402378366	13.1701738608004	0	0	0	0	0	11.50280852306	0	8.31771178485434	0	0	0	15.0261704271014	0	0
+MYO7A	0	0	10.2133954279646	0	0	0	0	0	15.8307316436531	0	0	0	0	0	0	0	0	13.7121952434523	15.9313225221491	0	0	0	0	0	0	0	0	16.8049477311572	0	0	0	0	0	0	0	13.1609986763417	0	0	0	0	0	0	0	0	0	0	8.83636708837122	0	0	0	17.463590172088	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9.1875306716268	0	0	13.5241872063119	18.0750354938906	0	0	10.2810788111136	17.2459745865081	15.9279160530013	12.748556401713	0	0	0	0	0
+DUSP14	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17.682339347864	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15.315185545429	13.7402034707105	0	0	0	0	0	0	0	0	0	13.0068022983915	16.2881643662067	0	0	9.93304513317431	0	0	0	0	0	0	16.1889386483903	0	0	0	0	0	0	0	0	14.2903113142977	0	0	0	0	0	0	0	0	0	8.92960758696251	0	0	0	0	0	9.58251231821503	0	0	0	0	0	0	0
+LSAMP	0	0	0	14.6759892692826	0	0	0	12.0533461710639	0	17.443105373872	0	0	0	0	18.0085029188716	14.9703906666539	0	0	0	0	15.1097945143932	16.4778545804206	0	10.3189090138321	0	0	16.8967216358908	10.0381235983496	0	0	16.5804778250305	0	14.0965479473356	15.1259052017533	0	0	14.4671092099988	0	15.3127843769133	0	7.58238867217773	17.0198239388304	0	0	0	8.04450047834992	0	0	0	0	0	13.968540182416	15.71562514092	15.2670695731409	0	0	16.0848565947262	16.8549278933251	0	0	15.0084279381472	0	0	0	0	9.64220443531159	12.2810179092402	17.0312914793051	12.2426279199397	14.4957467346967	17.5289904393214	0	0	0	0	17.4281796010913	7.97406042331398	0	0	0	17.2062943205767	9.24744364660748	0	0	9.1875306716268	0	0	0	0	0	17.2240719991621	18.2874179157258	0	0	0	0	0	13.639885471395	0	0
+IFRD2	0	14.1567591557826	0	0	14.957471072991	0	11.7467317882544	12.6777177703235	0	0	0	14.9692054355984	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	16.1887921858769	0	0	0	0	0	0	0	13.3325488559645	0	0	15.4049392399236	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11.9828942206529	0	0	0	0	0	0	0	0	0	0	0	0	0	15.220111460789	0	0	0	0	0	15.9054397866496
+PSMC3	0	13.2005548043296	14.8560845850134	13.9643699083462	0	0	15.3496874953813	10.7907868950769	0	15.1318370018154	0	9.04707783388214	0	8.19629321739164	8.79017289622793	0	0	15.8347317159755	0	0	0	17.0608232736151	0	0	0	13.5804315841045	0	16.8246657947268	0	0	0	0	14.0034440332771	13.6639750287706	9.87731250666145	15.9198563257041	14.9976043265065	8.23765146833625	14.0590768628974	0	0	9.47110050463318	0	0	0	15.9579116555843	14.8885374422562	0	0	9.20185308314151	17.7774040608022	15.4550410979026	0	0	0	12.7812138562999	13.3160965297846	13.362283927802	0	16.4148573168466	0	16.3937707725726	0	0	16.275541157128	7.77254179434776	16.4506691081895	0	17.0179871238337	0	0	12.4571973732293	0	18.4730583687277	0	0	0	14.7148366132387	0	14.1156444482226	0	0	0	0	0	0	14.2842702042516	0	0	16.3258394378728	16.0093455986421	0	0	12.9572206787611	0	0	0	13.4841036871113	0	9.22834347315191
+MUM1	0	0	0	12.6633325294353	0	0	0	14.5555669503357	0	13.3179500884142	0	0	0	0	16.5748276652721	0	0	0	0	0	13.6318200750724	0	0	12.710311816626	0	0	18.214454853308	15.1660730637326	0	0	0	0	14.7518697094683	7.00273235200855	0	0	14.1650955067633	0	0	0	0	0	0	13.2917085826559	0	0	12.2258260817879	0	0	0	0	0	0	11.886990211753	11.7235170132018	0	0	0	0	0	0	0	18.3760540871383	0	0	0	12.6529208030743	0	0	0	0	0	0	0	0	0	0	11.244072167057	0	0	0	0	14.4820702391067	14.2768099711357	0	16.0313326070449	16.1554843460377	0	0	15.7728280344041	10.6703592668752	0	0	13.6708456975204	0	0	0	13.8991097089352	0	0
+DIAPH2	0	0	0	0	14.2205357083466	16.7152640709125	0	0	0	0	0	0	0	16.654904535232	0	0	0	9.08248316789768	0	0	0	0	0	0	0	0	0	0	15.4373454971523	0	0	0	0	0	0	0	15.0941747307558	0	0	0	0	0	13.8406723774638	0	11.5418835561333	0	0	0	0	15.3892593189199	0	0	0	0	0	11.3076469757304	0	0	0	13.3508485655876	0	0	14.3317256961498	0	0	0	0	0	0	0	0	10.8056703376854	0	0	0	0	0	10.9546977217628	0	0	0	0	0	0	0	0	0	0	11.7742726683055	0	0	0	0	13.9279854762358	8.84459780169115	0	10.3514726687616	0	0	11.548346056541
diff -r 000000000000 -r baf7a079bce0 test-data/gene_stats.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gene_stats.tsv	Mon Jun 24 13:40:08 2019 -0400
@@ -0,0 +1,43 @@
+gene	mean	SD	Variance	Percentage_Detection
+ZNF454	0.922860300134436	3.46176149331655	11.9837926366092	7
+ACAD9	3.21757044598762	6.03354965169885	36.4037213995154	23
+LAIR1	5.14073096940228	7.67228689265092	58.8639861631431	32
+GAPDH	17.6727587681588	4.98787838098139	24.8789307434615	93
+CHTOP	4.95213087424945	6.69826385145611	44.8667386237237	37
+BAI3	1.40915813751371	4.12336508696455	17.0021396403981	11
+FAM63B	2.44551578150534	5.13806432586195	26.3997050166952	20
+TMEM132C	0.822592049405892	3.30504805041197	10.923342615532	6
+CNOT10	1.35116986328472	4.15039762997951	17.2258004869395	10
+NCAPH2	2.09924645828476	4.9160781393554	24.167824272248	16
+COQ7	1.81109934358668	4.59246883791874	21.0907700272547	14
+CDKN2A	3.14847608508595	5.97643617835182	35.7177893939125	22
+SIN3A	4.00526302988229	6.32973969419456	40.0656045962622	30
+SLC15A4	2.6490939213568	5.36541152568955	28.7876408400022	21
+BPHL	1.8725575575664	4.76402741808616	22.6959572402767	14
+H3F3C	2.69750936927498	4.35063868472497	18.9280569650254	29
+ISOC2	1.35653919273248	4.13500630208934	17.0982771183186	10
+PARVB	2.21851609168455	4.93366814223579	24.3410813377123	18
+CYTH4	3.15940473609362	6.446078714101	41.5519307883859	20
+ITGB1	5.73749610754924	6.96917363119079	48.569381101685	42
+TBC1D15	2.64803303609142	5.30241142820209	28.1155669539282	21
+SLC4A5	1.85823253159878	4.89934798569655	24.0036106849488	13
+CLPB	1.20688850619883	3.94292278228986	15.5466400671004	9
+RABL5	3.2703554589894	5.97444372569743	35.6939778315254	24
+C3orf62	2.21928690308303	5.23726221704512	27.4289155300884	16
+ZFHX4	2.71178769759176	5.4146903421813	29.3188715017114	21
+AKT1	3.4403135511678	6.3127111628083	39.8503222250445	24
+ZNF780B	1.00358719015216	3.48539676962484	12.1479906417113	8
+RNF185	1.46932887276529	4.13672007089318	17.1124529449304	12
+SMYD3	1.11766527425951	3.45565630150241	11.9415604741133	10
+CCT4	5.58991399452656	7.04582138621306	49.6435990064173	40
+OBFC2B	2.56257992189769	5.37946105314442	28.9386012222977	19
+APIP	1.48573169701519	4.42462910898839	19.5773427521074	11
+CHFR	3.2793294035845	6.00856983357212	36.1029114449129	24
+PSPH	3.45898367616203	5.82691731716674	33.9529654210976	27
+MYO7A	2.08943827729343	5.13674406841985	26.3861396244465	15
+DUSP14	1.34957110029642	4.17409370205428	17.4230582335292	10
+LSAMP	5.40538485683009	7.20340373028298	51.8890253014547	38
+IFRD2	1.56542610972806	4.50279575682847	20.2751696277125	11
+PSMC3	6.17973106872374	7.13113762893614	50.8531238828289	45
+MUM1	3.59113963428165	6.20728875372071	38.5304336720676	26
+DIAPH2	2.45173786931265	5.19109016758801	26.9474171280289	19
diff -r 000000000000 -r baf7a079bce0 test-data/signature.pdf
Binary file test-data/signature.pdf has changed
diff -r 000000000000 -r baf7a079bce0 test-data/signature.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/signature.tsv	Mon Jun 24 13:40:08 2019 -0400
@@ -0,0 +1,101 @@
+cell	score	rate	nGenes	total_counts
+1001000235.G10	3.91067297444198	LOW	5	77.9909221954615
+1001000174.B1	2.10477034315281	LOW	12	168.400445734346
+1001000177.C5	17.3373396414863	HIGH	11	159.937195211458
+1001000182.H4	4.10738125088592	LOW	14	192.634771492111
+1001000175.A2	8.44220431060683	HIGH	8	114.350084817451
+1001000230.B11	8.55876574549129	HIGH	5	79.5774386257488
+1001000237.E9	7.28301224420602	HIGH	15	201.765971829942
+1001000173.E10	2.10337163126214	LOW	15	201.227911442868
+1001000241.E7	8.19202003890676	HIGH	13	194.63692225468
+1001000249.A3	7.86252533808187	HIGH	13	186.873952274257
+1001000179.A7	8.17510090773342	HIGH	7	110.931451554681
+1001000247.F11	6.59043743407966	HIGH	14	155.769944463327
+1001000240.D9	3.96999174048949	LOW	5	73.5405420337799
+1001000178.G5	2.09541561385605	LOW	5	71.3112721859375
+1001000249.E3	2.09214340332731	LOW	10	132.36632558755
+1001000174.H6	7.66677807322868	HIGH	17	226.760822446058
+1001000181.F8	2.10709400933102	LOW	5	67.2424519090522
+1001000177.A10	7.59091943449932	HIGH	16	204.694215735197
+1001000235.D2	7.18077413419506	HIGH	10	143.430575780825
+1001000240.G10	3.96828356565184	LOW	4	68.9408902670553
+1001000248.E7	3.79680269738866	LOW	7	106.704357399606
+1001000012.B6	2.09064719814766	LOW	8	115.939391977434
+1001000179.H4	3.86977998672059	LOW	5	78.7940286817071
+1001000230.C1	3.84572709101563	LOW	9	129.591633959121
+1001000175.H9	2.10863142203113	LOW	8	114.115259209976
+1001000241.G11	4.19313861629077	LOW	8	117.738892714724
+1001000174.G2	2.08036012270756	LOW	4	69.3580162624446
+1001000252.C6	4.15779109562327	LOW	11	158.806427511089
+1001000186.D11	4.25199167750475	LOW	6	90.5743065128312
+1001000239.G7	1	LOW	3	53.8312977258561
+1001000258.G11	2.09764420198528	LOW	4	68.8136405730902
+1001000264.A1	1	LOW	3	50.3162837331849
+1001000174.A10	7.98562122525758	HIGH	15	208.015032616852
+1001000255.E9	2.10073269844653	LOW	11	149.820225707172
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