annotate scripts/estimateprops.R @ 4:56371b5a2da9 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
author bgruening
date Thu, 10 Feb 2022 12:52:31 +0000
parents fd7a16d073c5
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
1 suppressWarnings(suppressPackageStartupMessages(library(xbioc)))
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
2 suppressWarnings(suppressPackageStartupMessages(library(MuSiC)))
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
3 suppressWarnings(suppressPackageStartupMessages(library(reshape2)))
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
4 suppressWarnings(suppressPackageStartupMessages(library(cowplot)))
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
5 ## We use this script to estimate the effectiveness of proportion methods
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
6
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
7 ## Load Conf
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
8 args <- commandArgs(trailingOnly = TRUE)
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
9 source(args[1])
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
10
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
11 ## Estimate cell type proportions
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
12 est_prop <- music_prop(
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
13 bulk.eset = bulk_eset, sc.eset = scrna_eset,
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
14 clusters = celltypes_label,
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
15 samples = samples_label, select.ct = celltypes, verbose = T)
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
16
4
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
17
1
3ca0132c182a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
bgruening
parents: 0
diff changeset
18 estimated_music_props <- est_prop$Est.prop.weighted
3ca0132c182a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
bgruening
parents: 0
diff changeset
19 estimated_nnls_props <- est_prop$Est.prop.allgene
4
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
20 ##
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
21 estimated_music_props_flat <- melt(estimated_music_props)
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
22 estimated_nnls_props_flat <- melt(estimated_nnls_props)
0
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
23
3
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
24 scale_yaxes <- function(gplot, value) {
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
25 if (is.na(value)) {
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
26 gplot
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
27 } else {
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
28 gplot + scale_y_continuous(lim = c(0, value))
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
29 }
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
30 }
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
31
4
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
32 sieve_data <- function(func, music_data, nnls_data) {
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
33 if (func == "list") {
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
34 res <- list(if ("MuSiC" %in% methods) music_data else NULL,
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
35 if ("NNLS" %in% methods) nnls_data else NULL)
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
36 res[lengths(res) > 0] ## filter out NULL elements
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
37 } else if (func == "rbind") {
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
38 rbind(if ("MuSiC" %in% methods) music_data else NULL,
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
39 if ("NNLS" %in% methods) nnls_data else NULL)
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
40 } else if (func == "c") {
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
41 c(if ("MuSiC" %in% methods) music_data else NULL,
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
42 if ("NNLS" %in% methods) nnls_data else NULL)
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
43 }
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
44 }
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
45
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
46
0
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
47 ## Show different in estimation methods
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
48 ## Jitter plot of estimated cell type proportions
3
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
49 jitter_fig <- scale_yaxes(Jitter_Est(
4
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
50 sieve_data("list",
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
51 data.matrix(estimated_music_props),
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
52 data.matrix(estimated_nnls_props)),
1
3ca0132c182a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
bgruening
parents: 0
diff changeset
53 method.name = methods, title = "Jitter plot of Est Proportions",
3
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
54 size = 2, alpha = 0.7) + theme_minimal(), maxyscale)
0
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
55
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
56 ## Make a Plot
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
57 ## A more sophisticated jitter plot is provided as below. We separated
1
3ca0132c182a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
bgruening
parents: 0
diff changeset
58 ## the T2D subjects and normal subjects by their disease factor levels.
4
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
59 m_prop <- sieve_data("rbind",
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
60 estimated_music_props_flat,
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
61 estimated_nnls_props_flat)
1
3ca0132c182a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
bgruening
parents: 0
diff changeset
62 colnames(m_prop) <- c("Sub", "CellType", "Prop")
3ca0132c182a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
bgruening
parents: 0
diff changeset
63
3ca0132c182a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
bgruening
parents: 0
diff changeset
64 if (is.null(celltypes)) {
3ca0132c182a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
bgruening
parents: 0
diff changeset
65 celltypes <- levels(m_prop$CellType)
3ca0132c182a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
bgruening
parents: 0
diff changeset
66 message("No celltypes declared, using:")
3ca0132c182a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
bgruening
parents: 0
diff changeset
67 message(celltypes)
3ca0132c182a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
bgruening
parents: 0
diff changeset
68 }
0
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
69
1
3ca0132c182a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
bgruening
parents: 0
diff changeset
70 if (is.null(phenotype_factors)) {
3ca0132c182a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
bgruening
parents: 0
diff changeset
71 phenotype_factors <- colnames(pData(bulk_eset))
3ca0132c182a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
bgruening
parents: 0
diff changeset
72 }
3ca0132c182a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
bgruening
parents: 0
diff changeset
73 ## filter out unwanted factors like "sampleID" and "subjectName"
3ca0132c182a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
bgruening
parents: 0
diff changeset
74 phenotype_factors <- phenotype_factors[
3ca0132c182a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
bgruening
parents: 0
diff changeset
75 !(phenotype_factors %in% phenotype_factors_always_exclude)]
3ca0132c182a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
bgruening
parents: 0
diff changeset
76 message("Phenotype Factors to use:")
3
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
77 message(paste0(phenotype_factors, collapse = ", "))
0
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
78
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
79 m_prop$CellType <- factor(m_prop$CellType, levels = celltypes) # nolint
1
3ca0132c182a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
bgruening
parents: 0
diff changeset
80 m_prop$Method <- factor(rep(methods, each = nrow(estimated_music_props_flat)), # nolint
3ca0132c182a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
bgruening
parents: 0
diff changeset
81 levels = methods)
3
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
82
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
83 if (use_disease_factor) {
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
84
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
85 if (phenotype_target_threshold == -99) {
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
86 phenotype_target_threshold <- -Inf
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
87 message("phenotype target threshold set to -Inf")
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
88 }
4
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
89 ## the "2" here is to do with the sample groups, not number of methods
3
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
90 m_prop$Disease_factor <- rep(bulk_eset[[phenotype_target]], 2 * length(celltypes)) # nolint
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
91 m_prop <- m_prop[!is.na(m_prop$Disease_factor), ]
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
92 ## Generate a TRUE/FALSE table of Normal == 1 and Disease == 2
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
93 sample_groups <- c("Normal", sample_disease_group)
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
94 m_prop$Disease <- factor(sample_groups[(m_prop$Disease_factor > phenotype_target_threshold) + 1], # nolint
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
95 levels = sample_groups)
0
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
96
3
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
97 ## Binary to scale: e.g. TRUE / 5 = 0.2
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
98 m_prop$D <- (m_prop$Disease == # nolint
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
99 sample_disease_group) / sample_disease_group_scale
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
100 ## NA's are not included in the comparison below
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
101 m_prop <- rbind(subset(m_prop, Disease != sample_disease_group),
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
102 subset(m_prop, Disease == sample_disease_group))
0
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
103
4
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
104 jitter_new <- scale_yaxes(
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
105 ggplot(m_prop, aes(Method, Prop)) +
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
106 geom_point(aes(fill = Method, color = Disease,
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
107 stroke = D, shape = Disease),
3
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
108 size = 2, alpha = 0.7,
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
109 position = position_jitter(width = 0.25, height = 0)) +
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
110 facet_wrap(~ CellType, scales = "free") +
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
111 scale_colour_manual(values = c("white", "gray20")) +
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
112 scale_shape_manual(values = c(21, 24)) + theme_minimal(), maxyscale)
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
113
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
114 }
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
115
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
116 if (use_disease_factor) {
0
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
117
3
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
118 ## Plot to compare method effectiveness
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
119 ## Create dataframe for beta cell proportions and Disease_factor levels
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
120 ## - Ugly code. Essentially, doubles the cell type proportions for each
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
121 ## set of MuSiC and NNLS methods
4
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
122 m_prop_ana <- data.frame(
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
123 pData(bulk_eset)[rep(1:nrow(estimated_music_props), length(methods)), #nolint
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
124 phenotype_factors],
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
125 ## get proportions of target cell type
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
126 ct.prop = sieve_data("c",
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
127 estimated_music_props[, phenotype_scrna_target],
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
128 estimated_nnls_props[, phenotype_scrna_target]),
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
129 ##
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
130 Method = factor(rep(methods,
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
131 each = nrow(estimated_music_props)),
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
132 levels = methods))
3
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
133 ## - fix headers
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
134 colnames(m_prop_ana)[1:length(phenotype_factors)] <- phenotype_factors #nolint
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
135 ## - drop NA for target phenotype (e.g. hba1c)
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
136 m_prop_ana <- subset(m_prop_ana, !is.na(m_prop_ana[phenotype_target]))
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
137 m_prop_ana$Disease <- factor( # nolint
4
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
138 ## - Here we set Normal/Disease assignments across the methods
3
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
139 sample_groups[(
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
140 m_prop_ana[phenotype_target] > phenotype_target_threshold) + 1
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
141 ],
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
142 sample_groups)
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
143 ## - Then we scale this binary assignment to a plotable factor
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
144 m_prop_ana$D <- (m_prop_ana$Disease == # nolint
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
145 sample_disease_group) / sample_disease_group_scale
0
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
146
4
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
147 jitt_compare <- scale_yaxes(
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
148 ggplot(m_prop_ana, aes_string(phenotype_target, "ct.prop")) +
3
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
149 geom_smooth(method = "lm", se = FALSE, col = "black", lwd = 0.25) +
4
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
150 geom_point(aes(fill = Method, color = Disease,
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
151 stroke = D, shape = Disease),
3
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
152 size = 2, alpha = 0.7) + facet_wrap(~ Method) +
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
153 ggtitle(paste0(toupper(phenotype_target), " vs. ",
4
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
154 toupper(phenotype_scrna_target),
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
155 " Cell Type Proportion")) +
3
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
156 theme_minimal() +
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
157 ylab(paste0("Proportion of ",
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
158 phenotype_scrna_target, " cells")) +
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
159 xlab(paste0("Level of bulk factor (", phenotype_target, ")")) +
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
160 scale_colour_manual(values = c("white", "gray20")) +
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
161 scale_shape_manual(values = c(21, 24)), maxyscale)
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
162 }
0
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
163
1
3ca0132c182a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
bgruening
parents: 0
diff changeset
164 ## BoxPlot
4
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
165 plot_box <- scale_yaxes(Boxplot_Est(
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
166 sieve_data("list",
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
167 data.matrix(estimated_music_props),
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
168 data.matrix(estimated_nnls_props)),
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
169 method.name = methods) +
1
3ca0132c182a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
bgruening
parents: 0
diff changeset
170 theme(axis.text.x = element_text(angle = -90),
3ca0132c182a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
bgruening
parents: 0
diff changeset
171 axis.text.y = element_text(size = 8)) +
3
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
172 ggtitle(element_blank()) + theme_minimal(), maxyscale)
1
3ca0132c182a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
bgruening
parents: 0
diff changeset
173
3ca0132c182a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
bgruening
parents: 0
diff changeset
174 ## Heatmap
4
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
175 plot_hmap <- Prop_heat_Est(
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
176 sieve_data(
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
177 "list",
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
178 data.matrix(estimated_music_props),
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
179 data.matrix(estimated_nnls_props)),
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
180 method.name = methods) +
1
3ca0132c182a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
bgruening
parents: 0
diff changeset
181 theme(axis.text.x = element_text(angle = -90),
3ca0132c182a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
bgruening
parents: 0
diff changeset
182 axis.text.y = element_text(size = 6))
0
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
183
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
184 pdf(file = outfile_pdf, width = 8, height = 8)
3
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
185 if (length(celltypes) <= 8) {
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
186 plot_grid(jitter_fig, plot_box, labels = "auto", ncol = 1, nrow = 2)
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
187 } else {
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
188 print(jitter_fig)
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
189 plot_box
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
190 }
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
191 if (use_disease_factor) {
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
192 plot_grid(jitter_new, jitt_compare, labels = "auto", ncol = 1, nrow = 2)
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
193 }
1
3ca0132c182a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
bgruening
parents: 0
diff changeset
194 plot_hmap
3ca0132c182a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
bgruening
parents: 0
diff changeset
195 message(dev.off())
3ca0132c182a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
bgruening
parents: 0
diff changeset
196
4
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
197 writable <- function(obj, prefix, title) {
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
198 write.table(obj,
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
199 file = paste0("report_data/", prefix, "_",
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
200 title, ".tabular"),
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
201 quote = F, sep = "\t", col.names = NA)
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
202 }
1
3ca0132c182a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
bgruening
parents: 0
diff changeset
203
4
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
204 ## Output Proportions
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
205 if ("NNLS" %in% methods) {
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
206 writable(est_prop$Est.prop.allgene, "prop",
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
207 "NNLS Estimated Proportions of Cell Types")
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
208 }
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
209
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
210 if ("MuSiC" %in% methods) {
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
211 writable(est_prop$Est.prop.weighted, "prop",
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
212 "Music Estimated Proportions of Cell Types")
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
213 writable(est_prop$Weight.gene, "weightgene",
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
214 "Music Estimated Proportions of Cell Types (by Gene)")
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
215 writable(est_prop$r.squared.full, "rsquared",
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
216 "Music R-sqr Estimated Proportions of Each Subject")
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
217 writable(est_prop$Var.prop, "varprop",
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
218 "Matrix of Variance of MuSiC Estimates")
56371b5a2da9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 8beed1a19fcd9dc59f7746e1dfa735a2d5f29784"
bgruening
parents: 3
diff changeset
219 }
1
3ca0132c182a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
bgruening
parents: 0
diff changeset
220
0
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
221
3
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
222 if (use_disease_factor) {
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
223 ## Summary table of linear regressions of disease factors
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
224 for (meth in methods) {
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
225 ##lm_beta_meth = lm(ct.prop ~ age + bmi + hba1c + gender, data =
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
226 sub_data <- subset(m_prop_ana, Method == meth)
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
227
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
228 ## We can only do regression where there are more than 1 factors
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
229 ## so we must find and exclude the ones which are not
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
230 gt1_facts <- sapply(phenotype_factors, function(facname) {
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
231 return(length(unique(sort(sub_data[[facname]]))) == 1)
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
232 })
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
233 form_factors <- phenotype_factors
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
234 exclude_facts <- names(gt1_facts)[gt1_facts]
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
235 if (length(exclude_facts) > 0) {
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
236 message("Factors with only one level will be excluded:")
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
237 message(exclude_facts)
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
238 form_factors <- phenotype_factors[
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
239 !(phenotype_factors %in% exclude_facts)]
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
240 }
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
241 lm_beta_meth <- lm(as.formula(
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
242 paste("ct.prop", paste(form_factors, collapse = " + "),
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
243 sep = " ~ ")), data = sub_data)
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
244 message(paste0("Summary: ", meth))
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
245 capture.output(summary(lm_beta_meth),
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
246 file = paste0("report_data/summ_Log of ",
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
247 meth,
fd7a16d073c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
bgruening
parents: 1
diff changeset
248 " fitting.txt"))
1
3ca0132c182a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
bgruening
parents: 0
diff changeset
249 }
0
224721e76869 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 08c6fd3885bdfbf8b5c3f4dcc2d04729b577e3e1"
bgruening
parents:
diff changeset
250 }