Mercurial > repos > artbio > cpm_tpm_rpk
changeset 3:8b1020c25f0f draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 9149001c65de633ddfd2f91cf208074e40482ce3
| author | artbio |
|---|---|
| date | Fri, 12 Apr 2019 12:01:35 -0400 |
| parents | 563337e780ce |
| children | be358a1ebf67 |
| files | cpm_tpm_rpk.R cpm_tpm_rpk.xml test-data/none.tab test-data/none_pca.pdf test-data/none_tsne.pdf test-data/pca.nolab.pdf test-data/pca.pdf test-data/tsne.nolab.pdf test-data/tsne.pdf |
| diffstat | 9 files changed, 250 insertions(+), 11 deletions(-) [+] |
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--- a/cpm_tpm_rpk.R Wed Feb 06 19:31:57 2019 -0500 +++ b/cpm_tpm_rpk.R Fri Apr 12 12:01:35 2019 -0400 @@ -29,7 +29,7 @@ c("-t", "--type"), default = 'cpm', type = 'character', - help = "Transformation type, either cpm, tpm or rpk [default : '%default' ]" + help = "Transformation type, either cpm, tpm, rpk or none[default : '%default' ]" ), make_option( c("-s", "--sep"), @@ -127,7 +127,7 @@ } else if ((opt$type == "tpm" | opt$type == "rpk") & opt$gene == "") { stop("At least two arguments must be supplied (count data and gene length file).\n", call. = FALSE) -} else if (opt$type != "tpm" & opt$type != "rpk" & opt$type != "cpm") { +} else if (opt$type != "tpm" & opt$type != "rpk" & opt$type != "cpm" & opt$type != "none") { stop("Wrong transformation requested (--type option) must be : cpm, tpm or rpk.\n", call. = FALSE) } @@ -153,6 +153,7 @@ data = read.table( opt$data, + check.names = FALSE, header = opt$colnames, row.names = 1, sep = opt$sep @@ -177,6 +178,8 @@ res = as.data.frame(apply(data, 2, tpm, length = gene_length), row.names = rownames(data)) if (opt$type == "rpk") res = as.data.frame(apply(data, 2, rpk, length = gene_length), row.names = rownames(data)) +if (opt$type == "none") + res = data colnames(res) = colnames(data) @@ -206,7 +209,7 @@ embedding$Class <- as.factor(sub("Class_", "", rownames(tdf))) gg_legend = theme(legend.position="none") ggplot(embedding, aes(x=V1, y=V2)) + - geom_point(size=1.25, color='red') + + geom_point(size=1, color='red') + gg_legend + xlab("") + ylab("") + @@ -215,16 +218,20 @@ geom_text(aes(label=Class),hjust=-0.2, vjust=-0.5, size=2.5, color='darkblue') } ggsave(file=opt$tsne_out, device="pdf") - # make PCA and plot result with ggfortify + # make PCA and plot result with ggfortify (autoplot) tdf.pca <- prcomp(tdf, center = TRUE, scale. = T) if (opt$tsne_labels == TRUE) { - autoplot(tdf.pca, shape=F, label=T, label.size=2.5, colour="darkred") + + autoplot(tdf.pca, shape=F, label=T, label.size=2.5, label.vjust=1.2, + label.hjust=1.2, + colour="darkblue") + + geom_point(size=1, color='red') + xlab(paste("PC1",summary(tdf.pca)$importance[2,1]*100, "%")) + ylab(paste("PC2",summary(tdf.pca)$importance[2,2]*100, "%")) + ggtitle('PCA') ggsave(file=opt$pca_out, device="pdf") } else { - autoplot(tdf.pca, shape=T, colour="red") + + autoplot(tdf.pca, shape=T, colour="darkblue") + + geom_point(size=1, color='red') + xlab(paste("PC1",summary(tdf.pca)$importance[2,1]*100, "%")) + ylab(paste("PC2",summary(tdf.pca)$importance[2,2]*100, "%")) + ggtitle('PCA')
--- a/cpm_tpm_rpk.xml Wed Feb 06 19:31:57 2019 -0500 +++ b/cpm_tpm_rpk.xml Fri Apr 12 12:01:35 2019 -0400 @@ -1,4 +1,4 @@ -<tool id="cpm_tpm_rpk" name="Generate CPM, TPM, RPK" version="0.3.0"> +<tool id="cpm_tpm_rpk" name="Generate CPM, TPM, RPK" version="0.4.0"> <description>from raw counts expression values</description> <requirements> <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement> @@ -64,6 +64,7 @@ <option value="cpm" selected="true">CPM</option> <option value="tpm">TPM</option> <option value="rpk">RPK</option> + <option value="none">NONE</option> </param> <when value="tpm"> <param name="gene_file" type="data" format="txt" label="Gene length file"/> @@ -97,6 +98,8 @@ </when> <when value="cpm"> </when> + <when value="none"> + </when> </conditional> <param name="log" type="select" label="Data should be log transformed ?"> <option value="FALSE" selected="true">No</option> @@ -108,10 +111,10 @@ <option value="yes" >t-SNE and PCA</option> </param> <when value="yes"> - <param name="seed" value="49.0" type="float" label="Seed value for reproducibility" help="Set to 49 as default" /> - <param name="perp" value="10.0" type="float" label="perplexity" help="should be less than ((nbre observations)-1)/3" /> - <param name="theta" value="1.0" type="float" label="theta"/> - <param name="tsne_labels" type="select" label="Add labels to points in the t-SNE plot" > + <param name="seed" value="49.0" type="float" label="Seed value for reproducibility of t-SNE" help="Set to 49 as default" /> + <param name="perp" value="10.0" type="float" label="perplexity (t-SNE)" help="should be less than ((nbre observations)-1)/3" /> + <param name="theta" value="1.0" type="float" label="theta (t-SNE)"/> + <param name="tsne_labels" type="select" label="Add labels to points plots" > <option value="no" selected="true">No Labels</option> <option value="yes" >Label points</option> </param> @@ -136,6 +139,19 @@ <tests> <!-- test t-SNE --> <test> + <param name="input" value="none.tab" ftype="tabular"/> + <param name="type_transfo" value="none"/> + <param name="log" value="FALSE"/> + <param name="visualisation" value="yes"/> + <param name="seed" value="49"/> + <param name="perp" value="10"/> + <param name="theta" value="1" /> + <param name="tsne_labels" value="yes" /> + <output name="output" file="none.tab" ftype="tabular"/> + <output name="tsne_out" file="none_tsne.pdf" ftype="pdf"/> + <output name="pca_out" file="none_pca.pdf" ftype="pdf"/> + </test> + <test> <param name="input" value="counts.tab" ftype="tabular"/> <param name="type_transfo" value="cpm"/> <param name="log" value="TRUE"/>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/none.tab Fri Apr 12 12:01:35 2019 -0400 @@ -0,0 +1,216 @@ +Features 20nM_1 20sM_4 32nM_7 32sM_10 40nM_13 40sM_16 20n1d_a 20n1d_b 30n5h_c1 30n5h_c2 30s5h_c3 30s5h_c4 40n5h_c5 40n5h_c6 40s5h_c7 40s5h_c8 20n1d_c 20s1d_d 20s1d_e 20s1d_f 30n1d_g 30n1d_h 30n1d_i 30s1d_j 30s1d_k 30s1d_l 40n1d_m 40n1d_n 40n1d_o 40s1d_p 40s1d_q 40s1d_r +5S_DM 0 0 0 0 2.52271103749722 0 0 1.46876851779219 1.10607886502204 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.51278181441303 2.52260597944523 0 0 0 2.05794942496048 0.646139123391797 +ACCORD2_I-int 13.4694287027486 19.7873189245625 17.5674602110498 50.6988197972739 17.6589772624805 19.313391508794 18.1589910793351 13.2189166601297 12.1668675152425 18.2343843151734 26.0100186444685 27.0989940048899 23.1050300244153 31.4819885379018 24.4065408703064 27.0644930469596 9.83737686997288 16.0386739801143 14.5565923551731 13.0633061628418 25.016895793462 24.992288899494 17.9393955029792 28.3792668127381 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