Mercurial > repos > iuc > snpfreqplot

annotate heatmap_for_variants.R @ 0:469cc3aadaa7 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
author iuc
date Wed, 02 Dec 2020 21:22:37 +0000
parents
children 480821a403a0
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469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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1 #!/usr/bin/env R
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2
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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3 suppressPackageStartupMessages(library(pheatmap))
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4 suppressPackageStartupMessages(library(RColorBrewer))
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5 suppressPackageStartupMessages(library(tidyverse))
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6
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7 fapply <- function(vect_ids, func) {
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8 #' List apply but preserve the names
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9 res <- lapply(vect_ids, func)
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10 names(res) <- vect_ids
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11 return(res)
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12 }
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13
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14 # M A I N
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15 stopifnot(exists("samples"))
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16 variant_files <- fapply(samples$ids, read_and_process) # nolint
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17
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18 extractall_data <- function(id) {
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19 variants <- variant_files[[id]]
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20 tmp <- variants %>%
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21 mutate(posalt = uni_select) %>%
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22 select(posalt, AF)
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23 colnames(tmp) <- c("Mutation", id)
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24 return(tmp)
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25 }
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26
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27 extractall_annots <- function(id) {
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28 variants <- variant_files[[id]]
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29 tmp <- variants %>%
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30 mutate(posalt = uni_select,
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31 effect = EFF....EFFECT, gene = EFF....GENE) %>%
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32 select(posalt, effect, gene)
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33 return(tmp)
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34 }
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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35
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36 # process allele frequencies
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37 processed_files <- fapply(samples$ids, extractall_data)
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38 final <- as_tibble(
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39 processed_files %>%
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40 reduce(full_join, by = "Mutation", copy = T))
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41
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42 final <- final[str_order(final$Mutation, numeric = T), ] %>%
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43 column_to_rownames("Mutation") ## sort and set rownames
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44 final[final < variant_frequency] <- NA ## adjust the variant frequency:
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45 final <- final[rowSums(is.na(final)) != ncol(final), ]
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46 final <- t(final)
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47 final[is.na(final)] <- 0
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48 class(final) <- "numeric"
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49
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50 # add annotations
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51 ## readout annotations
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52 processed_annots <- fapply(samples$ids, extractall_annots)
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53 ann_final <- processed_annots %>%
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54 reduce(function(x, y) {
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55 unique(rbind(x, y))}) %>%
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56 filter(posalt %in% colnames(final)) ## apply frequency filter
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57 ann_final <- as_tibble(ann_final[str_order(
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58 ann_final$posalt, numeric = T), ]) %>%
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59 column_to_rownames("posalt") ## sort
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60
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61 # rename annotations
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62 trans <- function(x, mapping, replace_missing=NULL) {
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63 # helper function for translating effects
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64 mapped <- mapping[[x]]
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65 if (is.null(mapped)) {
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66 if (is.null(replace_missing)) x else replace_missing
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67 } else {
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68 mapped
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69 }
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70 }
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71
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72 # handle translation of classic SnpEff effects to sequence ontology terms
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73 # The following list defines the complete mapping between classic and So effect
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74 # terms even if not all of these are likely to appear in viral variant data.
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75 classic_snpeff_effects_to_so <- list(
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76 "coding_sequence_variant", "coding_sequence_variant", "disruptive_inframe_deletion", "disruptive_inframe_insertion", "inframe_deletion", "inframe_insertion", "downstream_gene_variant", "exon_variant", "exon_loss_variant", "frameshift_variant", "gene_variant", "intergenic_variant", "intergenic_region", "conserved_intergenic_variant", "intragenic_variant", "intron_variant", "conserved_intron_variant", "missense_variant", "rare_amino_acid_variant", "splice_acceptor_variant", "splice_donor_variant", "splice_region_variant", "5_prime_UTR_premature_start_codon_variant", "start_lost", "stop_gained", "stop_lost", "synonymous_variant", "start_retained_variant", "stop_retained_variant", "transcript_variant", "upstream_gene_variant", "3_prime_UTR_truncation_+_exon_loss_variant", "3_prime_UTR_variant", "5_prime_UTR_truncation_+_exon_loss_variant", "5_prime_UTR_variant", "initiator_codon_variant", "None", "chromosomal_deletion"
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77 )
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78 names(classic_snpeff_effects_to_so) <- c(
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79 "CDS", "CODON_CHANGE", "CODON_CHANGE_PLUS_CODON_DELETION", "CODON_CHANGE_PLUS_CODON_INSERTION", "CODON_DELETION", "CODON_INSERTION", "DOWNSTREAM", "EXON", "EXON_DELETED", "FRAME_SHIFT", "GENE", "INTERGENIC", "INTERGENIC_REGION", "INTERGENIC_CONSERVED", "INTRAGENIC", "INTRON", "INTRON_CONSERVED", "NON_SYNONYMOUS_CODING", "RARE_AMINO_ACID", "SPLICE_SITE_ACCEPTOR", "SPLICE_SITE_DONOR", "SPLICE_SITE_REGION", "START_GAINED", "START_LOST", "STOP_GAINED", "STOP_LOST", "SYNONYMOUS_CODING", "SYNONYMOUS_START", "SYNONYMOUS_STOP", "TRANSCRIPT", "UPSTREAM", "UTR_3_DELETED", "UTR_3_PRIME", "UTR_5_DELETED", "UTR_5_PRIME", "NON_SYNONYMOUS_START", "NONE", "CHROMOSOME_LARGE_DELETION"
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80 )
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81 # translate classic effects into SO terms leaving unknown terms (possibly SO already) as is
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parents:
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82 so_effects <- sapply(ann_final$effect, function(x) trans(x, classic_snpeff_effects_to_so))
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
83
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
84 # handle further translation of effects we care about
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
85 so_effects_translation <- list(
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
86 "non-syn", "syn",
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
87 "deletion", "deletion", "deletion",
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
88 "insertion", "insertion", "frame shift",
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
89 "stop gained", "stop lost"
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
90 )
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
91 names(so_effects_translation) <- c(
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
92 "missense_variant", "synonymous_variant",
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
93 "disruptive_inframe_deletion", "inframe_deletion", "chromosomal_deletion",
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
94 "disruptive_inframe_insertion", "inframe_insertion", "frameshift_variant",
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
95 "stop_gained", "stop_lost"
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
96 )
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
97 # translate to our simple terms turning undefined terms into '?'
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
98 simple_effects <- sapply(so_effects, function(x) trans(x, so_effects_translation, replace_missing = "?"))
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
99 # complex variant effects (those that do more than one thing) are concatenated
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
100 # with either '+' (for classic terms) or '&' (for SO terms)
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
101 simple_effects[grepl("+", so_effects, fixed = TRUE)] <- "complex"
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
102 simple_effects[grepl("&", so_effects, fixed = TRUE)] <- "complex"
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
103 simple_effects[so_effects == ""] <- "non-coding"
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
104
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
105 ann_final$effect <- simple_effects
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
106 ann_final$gene <- sub("^$", "NCR", ann_final$gene)
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
107
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
108 ## automatically determine gaps for the heatmap
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
109 gap_vector <- which(!(ann_final$gene[1:length(ann_final$gene) - 1] == # nolint
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
110 ann_final$gene[2:length(ann_final$gene)]))
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
111
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
112 # colormanagement
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
113 my_colors <- colorRampPalette(c("grey93", "brown", "black")) #heatmap
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
114 count <- length(unique(ann_final$gene)) #annotations (genes)
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
115 gene_color <- c(brewer.pal(brewer_color_gene_annotation, n = count))
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
116 names(gene_color) <- unique(ann_final$gene)
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
117
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
118 # colormanagement annotations (effect)
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
119 ## Define the full set of colors for each effect that we can encounter
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
120 ## This is not bulletproof. The effect names given here were swapped into the
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
121 ## data (see above substitutions in ann_final$effect) and so are hard-coded,
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
122 ## as well as their preferred colors.
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
123
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
124 all_colors <- data.frame(
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
125 color = c("white", "green", "orange", "red",
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
126 "black", "grey", "yellow", "blue", "purple", "brown"),
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
127 name = c("non-coding", "syn", "non-syn", "deletion",
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
128 "frame shift", "stop gained", "stop lost", "insertion",
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
129 "complex", "?"))
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
130 ## Reduce the full set to just those that we want
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
131 detected_effects <- unique(ann_final$effect)
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
132 subset_colors <- subset(all_colors, name %in% detected_effects)
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
133 effect_color <- subset_colors$color
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
134 names(effect_color) <- subset_colors$name
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
135 color_list <- list(gene_color = gene_color, effect_color = effect_color)
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
136 names(color_list) <- c("gene", "effect")
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
137
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
138 # visualize heatmap
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
139 if (pheat_number_of_clusters > length(samples$ids)) {
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
140 print(paste0("[INFO] Number of clusters: User-specified clusters (",
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
141 pheat_number_of_clusters,
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
142 ") is greater than the number of samples (",
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
143 length(samples$ids), ")"))
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
144 pheat_number_of_clusters <- length(samples$ids)
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
145 print(paste0("[INFO] Number of clusters: now set to ",
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
146 pheat_number_of_clusters))
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
147 }
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
148
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
149 get_plot_dims <- function(heat_map) {
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
150 ## get the dimensions of a pheatmap object
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
151 ## useful for plot formats that can't be written to a file directly, but
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
152 ## for which we need to set up a plotting device
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
153 ## source: https://stackoverflow.com/a/61876386
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
154 plot_height <- sum(sapply(heat_map$gtable$heights,
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
155 grid::convertHeight, "in"))
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
156 plot_width <- sum(sapply(heat_map$gtable$widths,
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
157 grid::convertWidth, "in"))
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
158 return(list(height = plot_height, width = plot_width))
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
159 }
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
160
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
161 height <- round(max(c(max(c(
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
162 16 * (length(unique(ann_final$effect)) +
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
163 length(unique(ann_final$gene))), 160)) /
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
164 nrow(final), 15)))
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
165 width <- round(ratio * height)
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
166
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
167
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
diff changeset
168 if (!(out_ext %in% c("svg", "jpeg", "png", "pdf"))) {
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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169 stop("Unknown extension: ", ext, ", aborting.")
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170 }
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
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171 plot_device <- get(out_ext)
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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172
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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173
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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174 ## A constant scaling factor based on the calculated dimensions
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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175 ## above does not work for PNG, so we resort to feeding pheatmap
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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176 ## with a direct filename
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
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177 plot_filename <- NA
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
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178 if (out_ext %in% c("jpeg", "png")) {
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
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179 plot_filename <- out_file
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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180 }
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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181
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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182 ## SVG is not a format pheatmap knows how to write to a file directly.
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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183 ## As a workaround we
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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184 ## 1. create the plot object
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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185 ## 2. get its dimensions
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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186 ## 3. set up a svg plotting device with these dimensions
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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187 ## 4. print the heatmap object to the device
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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188 hm <- pheatmap(
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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189 final,
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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190 color = my_colors(100),
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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191 cellwidth = width,
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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192 cellheight = height,
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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193 fontsize_col = round(1 / 3 * width),
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
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194 fontsize_row = round(1 / 3 * min(c(height, width))),
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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195 clustering_method = pheat_clustering_method,
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196 cluster_rows = pheat_clustering,
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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197 cluster_cols = F,
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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198 cutree_rows = pheat_number_of_clusters,
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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199 annotation_col = ann_final,
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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200 annotation_colors = color_list,
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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201 filename = plot_filename,
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
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202 gaps_col = gap_vector
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
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203 )
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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204
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
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205 if (out_ext %in% c("pdf", "svg")) {
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
parents:
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206 plot_dims <- get_plot_dims(hm)
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
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207 plot_device(out_file,
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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208 width = plot_dims$width,
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
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209 height = plot_dims$height)
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
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210 print(hm)
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
iuc
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211 dev.off()
469cc3aadaa7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1f35303af979c16d9a3126dbc882a59f686ace5d"
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212 }