Commit 4a9b12be authored by Holger Brandl's avatar Holger Brandl

fixed intercept parameter name when using geom_vline

parent 273a9193
......@@ -81,12 +81,12 @@ deResults %>% with(as.data.frame(table(sample_1, sample_2)))
#+ fig.width=20, fig.height=18
deResults %>% ggplot(aes(log2FoldChange)) +
geom_histogram(binwidth=0.1) +
facet_grid(sample_1 ~ sample_2) + geom_vline(yintercept=0, color="blue") +
facet_grid(sample_1 ~ sample_2) + geom_vline(xintercept=0, color="blue") +
xlim(-4,4)
deResults %>% ggplot(aes(pvalue)) +
geom_histogram() +
facet_grid(sample_1 ~ sample_2) + geom_vline(yintercept=0.01, slope=1, color="blue")
facet_grid(sample_1 ~ sample_2) + geom_vline(xintercept=0.01, slope=1, color="blue")
### see https://www.biostars.org/p/80448/ for Pairwise Comparison
#res <- results(dds, contrast=c(c("condition","H1M_Dome","H1M_Shield")))
......
......@@ -61,7 +61,7 @@ peaks %>%
ggplot(aes(peak_width)) +
geom_histogram() +
facet_grid(sample ~ peak_type) +
# + geom_vline(yintercept=0, color="blue")
# + geom_vline(xintercept=0, color="blue")
ggtitle("peak width distribution") +
xlim(0,1000)
......@@ -71,7 +71,7 @@ peaks %>%
geom_jitter(alpha=0.05, data=sample_frac(peaks, 0.1)) +
geom_violin(alpha=0.8) +
facet_wrap(~ peak_type) +
# + geom_vline(yintercept=0, color="blue")
# + geom_vline(xintercept=0, color="blue")
ggtitle("peak width distribution") +
ylim(0,1000)
......@@ -82,7 +82,7 @@ peaks %>%
geom_jitter(alpha=0.05, data=sample_frac(peaks, 0.1)) +
geom_violin(alpha=0.8) +
facet_wrap(~ peak_type) +
# + geom_vline(yintercept=0, color="blue")
# + geom_vline(xintercept=0, color="blue")
ggtitle("peak score distribution") +
ylim(0,100) +
rot_x_lab()
......
......@@ -135,8 +135,8 @@ rend.R -e $NGS_TOOLS/common/cp_enrichment.R --overlay_expr_data ../plot_score_ma
## bidirectional sync with project space
## todo define mount path on bioinfo for bidirectional synching
~/bin/unison $baseDir ssh://bioinfo///home/brandl/mnt/<<MOUNT_PATH>> -fastcheck true -times -perms 0
## ~/bin/unison $baseDir ssh://bioinfo///home/brandl/mnt/<<MOUNT_PATH>> -fastcheck true -times -perms 0
# uni-directional sync
# or use a uni-directional sync
#rsync -avsn --delete $baseDir brandl@fileserver:/projects//file/server/path
mailme "$project: sync done"
\ No newline at end of file
......@@ -225,7 +225,7 @@ deResults <- adply(contrasts, 1, splat(function(sample_1, sample_2){
deResults %>% ggplot(aes(s1_over_s2_logfc)) +
geom_histogram(binwidth=0.1) +
facet_grid(sample_1 ~ sample_2) + geom_vline(yintercept=0, color="blue") +
facet_grid(sample_1 ~ sample_2) + geom_vline(xintercept=0, color="blue") +
xlim(-2,2) +
ggtitle("sample1 over sampl2 logFC ")
......@@ -236,13 +236,13 @@ deResults %>% ggplot(aes(s1_over_s2_logfc)) +
#deResults %>% ggplot(aes(pvalue)) +
# geom_histogram() +
# xlim(0,1) +
# facet_grid(sample_1 ~ sample_2) + geom_vline(yintercept=0.01, slope=1, color="blue") +
# facet_grid(sample_1 ~ sample_2) + geom_vline(xintercept=0.01, slope=1, color="blue") +
# ggtitle("p-value distributions") #+ scale_x_log10()
#
#deResults %>% ggplot(aes(padj)) +
# geom_histogram() +
## xlim(0,1) +
# facet_grid(sample_1 ~ sample_2) + geom_vline(yintercept=0.01, slope=1, color="blue") +
# facet_grid(sample_1 ~ sample_2) + geom_vline(xintercept=0.01, slope=1, color="blue") +
# ggtitle("Adjusted p-value distributions") #+ scale_x_log10()
......
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