Skip to content
Permalink
Branch: master
Find file Copy path
Find file Copy path
Fetching contributors…
Cannot retrieve contributors at this time
120 lines (95 sloc) 4.61 KB
# --------- REQUIRED SETTINGS --------------
# example config file with all possible settings
# For a minimal file, see minimal.conf
# internal short name, only visible in the URL
# same as the output directory name
# no special chars, no whitespace, please
name = "sample"
# priority determines the order of the datasets
# smallest comes first
priority = 10
# tags are shown in the dataset browser
# current tags:
# smartseq2,10x
tags = ["smartseq2"]
# human-readable name of this dataset
shortLabel="CellBrowser 100-genes demo"
# name of the expression matrix file, genes are rows
exprMatrix="exprMatrix.tsv.gz"
# "gencode-human", "gencode-mouse" or "symbol"
# For "symbol" you can specify which database to use to check
# symbols or, for cbHub, how to map them to the genome.
# 'auto' will automatically detect Ensembl human/mouse IDs
# and translate to symbols
geneIdType="auto"
# name of the meta data table ("samplesheet). One sample per row. First row is name of sample.
meta="meta.tsv"
# we try to auto-detect the field type of fields in the meta data.
# Sometimes, this doesn't work, e.g. when your cluster ID is a numer
# or your C1 chip ID is a number, but you don't want them binned, you want
# to treat as if they were categories
enumFields = ["c1_cell_id"]
# tsv files with coordinates of every sample in format <sampleId, x, y>
# first the name of the file, then a human readable description
coords=[
{
"file":"tsne.coords.tsv",
"flipY" : False, # R/Matplotlib files need to be flipped on the Y-axis
"shortLabel":"t-SNE on WGCNA"
},
# you can force coloring of some other meta data field when a layout is changed to another one
{
"file":"subset.coords.tsv",
"shortLabel":"neural cells",
# you can overlay lines onto the cells, table has to have columns named x1, x2, y1, y2
"lineFile" : "lines.tsv",
# you can flip the y-axis of just the lines, relative to the points
"lineFlipY" : True,
"colorOnMeta":"neuralCluster"
},
]
# --------- OPTIONAL SETTINGS --------------
# default field in the meta data table with the name of the cluster
clusterField="WGCNAcluster"
# default field in the meta data table used for the label of the clusters shown by default
labelField="WGCNAcluster"
# tsv files with marker gene lists for the clusters
# format is (clusterName, geneSymbol, pValue, enrichment) + any additional fields or URLs you want to show
markers=[
{"file":"markers.tsv", "shortLabel":"Cluster-specific markers"}
]
# optional: UCSC track hub with the BAM file reads and expression values
# Alternatively, you can also provide a full link to a UCSC Genome Browser session here
hubUrl="http://cells.ucsc.edu/cortex-dev/hub/hub.txt"
# optional: table with <name><color> for any meta data values
# color is a six-digit hexcode
# name is a any value in the meta data table, e.g. cluster name. Canb be a .tsv or .csv file.
colors="colors.tsv"
# should the cluster labels be shown by default (default: true)
showLabels=True
# the radius of the circles. If not specified, reasonable defaults will be used
#radius = 5
# the alpha/transparency of the circles. If not specified, reasonable defaults will be used.
#alpha = 0.3
# you need short names for your clusters, as there is little space on the plot
# but cell types have complicated and long names
# So you can provide a table with two columns: 1) short cluster name 2) long version
# e.g. EC, endothelial cells
# can be a .tsv or .csv file
acronymFile = "acronyms.tsv"
# genes that are highlighted in your paper can be pre-loaded and are shown as a clickable table on the left
quickGenesFile = "quickGenes.csv"
# the unit of the values in the expression matrix
# any string, shown on genome browser and violin y-Axis
# typical values are: "read count/UMI", "log of read count/UMI", "TPM", "log of TPM", "CPM", "FPKM", "RPKM"
unit = "TPM"
# format of the numbers in the matrix.
# 'auto' works in 99% of the cases. Otherwise you can use 'int' for integers and 'float' for floating point numbers.
# Use 'forceInt' if your matrix contains only integers but in a format like 3.123e10
# or the matrix has only integers expressed like 100.000, 200.000, 300.00, ...
matrixType='auto'
# --- The following options are only used by cbHub ---
hubName = "100 Genes Sample Hub" # name of hub (optional, default is value of 'shortLabel')
ucscDb = "hg38" # UCSC genome ID of the BAM files, required
bamDir = "bam" # directory with .bam files, optional. If not present, don't do bam merging
#clusterOrder = "clusterOrder.txt" # file with cluster names to order the tracks (default is alphabetical)
You can’t perform that action at this time.