Description Usage Format Examples
Sashimi plot files data.frame for Farris data
1 |
data.frame suitable for use with
splicejam::prepareSashimi()
for the filesDF
argument.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 | #farris_sashimi_files_df
base_url <- "https://orio.niehs.nih.gov/ucscview/farrisHub/mm10/";
factor1 <- c("CA1", "CA2", "CA3", "DG");
factor2 <- c("CB", "DE");
junc_suffix <- ".STAR_mm10.combinedJunctions.bed.gz";
junc_urls <- paste0(base_url,
rep(factor1, each=2),
"_",
rep(factor2, 4),
junc_suffix);
junc_sample_id <- paste(rep(factor1, each=2),
rep(factor2, 4),
sep="_");
junc_scale_factors <- 2^c(
CA1_CB=-0.185,
CA1_DE=0.146,
CA2_CB=-0.241,
CA2_DE=0.765,
CA3_CB=-0.215,
CA3_DE=0.256,
DG_CB=-0.376,
DG_DE=0.372);
junc_df <- data.frame(sample_id=junc_sample_id,
url=junc_urls,
type="junction",
scale_factor=junc_scale_factors[junc_sample_id]);
if (suppressPackageStartupMessages(require(knitr))) {
knitr::kable(junc_df)
} else {
junc_df;
}
bw_factor1 <- c(factor1);
bw_factor2 <- c(factor2);
bw_base_url <- paste0(base_url, "union_bigwig/");
bw_strand <- c("pos", "neg");
bw_suffix <- ".bw";
bw_urls <- paste0(
rep(bw_factor1, each=4),
"_",
rep(bw_factor2, each=2),
".union.",
bw_strand,
bw_suffix
);
bw_scale_factors <- 2^c(
CA1_CB=-0.0157,
CA1_DE=0.306,
CA2_CB=-0.0266,
CA2_DE=0.0947,
CA3_CB=0.00839,
CA3_DE=0.528,
DG_CB=-0.243,
DG_DE=-0.283);
if (suppressPackageStartupMessages(require(knitr))) {
knitr::kable(as.data.frame(matrix(bw_urls, ncol=5)))
} else {
as.data.frame(matrix(bw_urls, ncol=4));
}
# remove NA entries
bw_url <- jamba::rmNA(bw_urls);
bw_sample_id <- gsub("^.*(CA[123]|DG)[_]*(CB|DE).*",
"\\1_\\2",
bw_url);
bw_df <- data.frame(
url=paste0(bw_base_url, bw_url),
sample_id=bw_sample_id,
type="bw",
scale_factor=bw_scale_factors[bw_sample_id]);
bw_df <- bw_df[do.call(order, bw_df[,c(2,1,3)]),];
farris_sashimi_files_df <- rbind(
junc_df,
bw_df);
# replace missing scale_factor with 1, should not be necessary
farris_sashimi_files_df$scale_factor[is.na(farris_sashimi_files_df$scale_factor)] <- 1;
farris_sashimi_files_df$CellType <- factor(
gsub("_.+", "",
farris_sashimi_files_df$sample_id),
levels=factor1);
farris_sashimi_files_df$Compartment <- factor(
gsub("^.+_", "",
farris_sashimi_files_df$sample_id),
levels=factor2);
if (suppressPackageStartupMessages(require(knitr))) {
knitr::kable(farris_sashimi_files_df)
} else {
farris_sashimi_files_df;
}
table(farris_sashimi_files_df[,c("CellType", "Compartment", "type")]);
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